Breeding Bird Surveys - Cleveland Metroparks

Nathan W. Byer

8/18/2022

The dataset

Tim Krynak, Erik Shaffer, Jen Brumfield, and other Cleveland Metroparks and affiliated colleagues conducted Breeding Bird Surveys (BBS) at a total of 211 routes between 2017 and 2021. 164 of these routes overlapped with long-term vegetation monitoring efforts through the Cleveland Metroparks Plant Community Assessment Program (PCAP). This provided an excellent opportunity to explore the potential relationships between vegetative composition, landscape structure, and breeding bird ecology and community composition.

Initial processing

First, we just read in the full BBS dataset. For our purposes, we will remove any BBS observations not paired with PCAP plots. We can also visualize the distribution of survey effort through time.

CMP_bbs_pcap_join<-read.csv("G:/NaturalResources/Byer/datasets/BBS/CMP_bbs_pcapjoin_elimWC_EATO.csv",header=T)
CMP_bbs_pcap_join_pcaponly<-CMP_bbs_pcap_join[!is.na(CMP_bbs_pcap_join$Plot.ID),]

datetime<-strptime(CMP_bbs_pcap_join_pcaponly$survey_cre,format="%m/%d/%Y %H:%M")
hist(datetime,breaks="months")

pcap_1styear_landscape<-read.csv("G:/NaturalResources/Byer/datasets/BBS/pcap_4yr_landscape_variables_202204281228.csv",header=T)

Next, we need to start grouping this dataset for downsteram analysis. This involves summarizing counts of each species for each plot. We also replace any NA values in the data frame with zeroes - this will be important for downstream applications, as we want to distinguish between unobserved species at a plot and check (typically coded 0s) and checks that were “skipped” (NAs).

CMP_bbs_pcap_join_pcaponly_pcapsum<-CMP_bbs_pcap_join_pcaponly %>% 
  group_by(simp_plot, reservatio,community,species_4_) %>%
  summarise(n=n(),longitude=mean(xcoord), latitude=mean(ycoord),vibifq=mean(vibi_fq),vibifqnotrees=mean(vibi_fq_no_trees),carex=mean(carex_metric_value),cyper=mean(cyperaceae_metric_value),
            dicot=mean(dicot_metric_value),shade=mean(shade_metric_value),shrub=mean(shrub_metric_value),
            hydro=mean(hydrophyte_metric_value),svp=mean(svp_metric_value),ap=mean(ap_ratio_metric_value),
            fqi=mean(fqai_score),bryo=mean(bryophyte_metric_value),hydro_rel=mean(hydrophyte_rel_cov_metric_value),
            hydro_rel_notrees=mean(hydrophyte_rel_cov_no_trees),
            sens_rel=mean(sensitive_rel_cov_metric_value),
            sens_rel_notree=mean(sensitive_rel_cov_no_trees),
            tol_rel=mean(tolerant_rel_cov_metric_value),
            tol_rel_notree=mean(tolerant_rel_cov_no_trees),
            inv=mean(invasive_graminoids_metric_value),
            small_tree=mean(small_tree_metric_value),
            subcanopy=mean(subcanopy_iv),
            canopy=mean(canopy_iv.1)
            ) %>%
  spread(species_4_,n) %>%
  replace(is.na(.),0)

names(pcap_1styear_landscape)[names(pcap_1styear_landscape) == 'site.name'] <- 'simp_plot'


CMP_bbs_pcap_join_pcaponly_pcapsum_landscape<-left_join(x = CMP_bbs_pcap_join_pcaponly_pcapsum,y = pcap_1styear_landscape,by="simp_plot")

CMP_bbs_pcap_join_pcaponly_pcapsum<-column_to_rownames(CMP_bbs_pcap_join_pcaponly_pcapsum_landscape,var="simp_plot")

This is a pretty unwieldly dataset at present - we have 164 rows (representing our BBS/PCAP plots) and 131 columns. Out of those 131 columns, 103 are unique species (designated with four-letter codes), so most of the first 27 covariates are essentially our “predictors” - in this case, our PCAP data.

Let’s do a bit more processing on this dataset to get it in shape for downstream analyses. First, we will separate out our bird community data.

birdcomm<-CMP_bbs_pcap_join_pcaponly_pcapsum[,28:(130)]

birdcomm[is.na(birdcomm)] <- 0

Next, we separate out our PCAP data.

vegecomm<-CMP_bbs_pcap_join_pcaponly_pcapsum[,5:26]

Finally, we will separate out the 1st year landscape covariates. As a quick note, these will not be strictly comparable with the 2nd survey landscape covariates, but should be pretty close (~5 years is likely not enough for substantial land cover change).

landcomm<-CMP_bbs_pcap_join_pcaponly_pcapsum[,142:153]

landcomm[is.na(landcomm)] <- 0

Since we are using the PCAP dataset as predictors here, we should likely check for correlations between these covariates. I have selected a (semi-)arbitrary cut-off of 0.6 to identify covariates as correlated; we then drop any covariates that are likely redundant.

vegecomm_cor<-cor(vegecomm)

set.seed(12345)
corvar<-findCorrelation(vegecomm_cor,cutoff=0.6)

vegecomm_drop<-vegecomm[,-corvar]

We can also check for correlations between the landscape covariates.

landcomm_cor<-cor(landcomm)

set.seed(12345)
corvar_land<-findCorrelation(landcomm_cor,cutoff=0.6)

landcomm_drop<-landcomm[,-corvar_land]

We can then check correlations between PCAP and landscape covariates.

landvegcomm_drop<-cbind(vegecomm_drop,landcomm_drop)

landvegcomm_drop_cor<-cor(landvegcomm_drop)

set.seed(12345)
corvar_landveg<-findCorrelation(landvegcomm_drop_cor,cutoff=0.6)

No covariates were overly correlated in this dataset, so we can proceed.

Now, we have:

  1. a vegecomm dataset - which representing PCAP measurements for each of the 164 BBS/PCAP plots.
  2. a birdcomm dataset - representing presence/absence of each bird species for each survey in each plot.
  3. a landcomm dataset - representing landscape covariates associated with these PCAP plots.

Note that we are not explicitly considering differences in bird counts (or occupancy, or detectability) through time at this point - we will get to that later. For now, we just want to explore broad associations between these two datasets!

Note as of 6/13/2022 - we will also want to only work with only binary data.

Community analyses

When working with datasets like these, we first have to acknowledge that these datasets are multivariate - with many possible predictor covariates (for example, plot-level characteristics) and many possible response covariates (for example, presence/absence of species in a plot). Fortunately, community ecology as a field has developed a number of standard approaches for exploring multivariate datasets, of which the most common is (arguably!) ordination. In essence, ordination techniques try to shrink down highly multidimensional datasets into a more manageable number of dimensions - often just a handful (and for initial plotting, typically just two). There are many, many possible ordination tools available for exploring community ecological datasets, and we will explore a few.

unconstrained ordination

In this section, we will be exploring ways of exploring the bird dataset on its own - basically, without any predictors.

First, we must reclassify our bird community data onto a binary scale - ranging from 0 (no detection) to 1 (detection).

We also set our color palette for residency status, so that Red = resident, Green = short-distance migrant, and Blue = neotropical migrant.

birdcomm_bin<-birdcomm

birdcomm_bin<- birdcomm_bin %>% mutate_if(is.numeric, ~1 * (. >= 1))

BBSMigrants<-read.csv("G:/NaturalResources/Byer/datasets/BBS/BBS Migants.csv",header=T)

BBSMigrants_sub<-BBSMigrants[BBSMigrants$SpeciesCode %in% colnames(birdcomm_bin),]

Residency<-BBSMigrants_sub$Residency

color_resid<-Residency

color_resid[color_resid %in% "NE"]<-"blue"

color_resid[color_resid %in% "M"]<-"green"

color_resid[color_resid %in% "R"]<-"red"

BBSMigrants_sub$color_resid<-color_resid

One of the most common approaches for unconstrained ordination is called Principal Components Analysis (PCA). I have illustrated vegan’s rda() function (which we will use a bit more below!). Out of the available options, I find rda() to be much easier to use, so I tend to use it preferentially. Here is a plot with convex hulls and points colored by reservation.

while a bit hard to interpret, plots within Rocky River (RR) seem to be the most variable - and it might be that we see higher diversity in that area. We will see as we proceed if that is true.

metric multidimensional scaling (Principal Coordinates Analysis)

You can think of this as a distance-based analog to PCA. In this case, since we are using Bray-Curtis distances on binary data (presence/absence), this is equivalent to Sorensen’s index.

non-metric multidimensional scaling

bird species most associated with community differences

We can also look at which birds are most differentiated across communities for both the PCOA and NMDS ordinations. The below code essentially a) relates individual bird presence/absence to the final PCOA ordination, b) extracts p-values for associations with MDS1 and 2 (the first two ordination axes), and c) selects only those birds that are most differentiated at p less than or equal to 0.001. We will do so for the PCA, PCOA, and NMDS.

For all of these analyses, keep in mind that these are differentiated across plots, rather than reservations. We will explore a way to identify reservation-level differentiated species a litle bit below.

Here is the PCA:

##    species         PC1           PC2 pvals
## 1     ACFL -0.69716294 -0.1508935718 0.001
## 2     AMCR -0.24666198 -0.2963413159 0.001
## 3     AMGO  0.09382893 -0.2841531898 0.001
## 4     AMKE  0.38723531 -0.2455200453 0.001
## 5     BAOR  0.46434543 -0.1374142804 0.001
## 6     BARS  0.47425412 -0.2189233645 0.001
## 7     BCCH -0.25735224 -0.3604541492 0.001
## 8     BGGN -0.21605918 -0.2719538252 0.001
## 9     BHCO  0.17428135 -0.2790791107 0.001
## 10    BRTH  0.41973857 -0.0869533026 0.001
## 11    CANG  0.15587408 -0.2491690243 0.001
## 12    CEDW  0.50170158 -0.0806099475 0.001
## 13    COGR  0.45349980  0.1690696909 0.001
## 14    COYE  0.48298960 -0.2005910142 0.001
## 15    DEJU -0.35182512 -0.2234465042 0.001
## 16    EABL  0.21626153 -0.3348356997 0.001
## 17    EAKI  0.44209119 -0.2979537624 0.001
## 18    EAME  0.32949356 -0.4853999033 0.001
## 19    EAWP -0.52013724 -0.3050792447 0.001
## 20    EUST  0.64151056 -0.0626558506 0.001
## 21    FISP  0.25701439 -0.2476275133 0.001
## 22    GCFL -0.07114924 -0.3336146265 0.001
## 23    GRCA  0.51950507 -0.0464609980 0.001
## 24    HAWO -0.26479071 -0.3078359029 0.001
## 25    HOSP  0.32094904  0.1140673835 0.001
## 26    HOWA -0.44170756 -0.4240075369 0.001
## 27    HOWR  0.31383507 -0.1488100390 0.001
## 28    INBU  0.30394564 -0.3598407644 0.001
## 29    KILL  0.34044627 -0.2474971881 0.001
## 30    MODO  0.54350836 -0.2372128158 0.001
## 31    NOFL  0.32814765 -0.2185413306 0.001
## 32    NRWS  0.36829543 -0.0329679429 0.001
## 33    OROR  0.68797727  0.0475092454 0.001
## 34    PIWO -0.21798535 -0.2947734707 0.001
## 35    RBGR  0.29323586 -0.2267343583 0.001
## 36    REVI -0.38049218 -0.3368389029 0.001
## 37    RWBL  0.64080597 -0.0549021700 0.001
## 38    SCTA -0.53238990 -0.3546866667 0.001
## 39    SOSP  0.56532468 -0.1184872259 0.001
## 40    TRES  0.56126450 -0.1531979241 0.001
## 41    TUVU  0.24506841 -0.3094927503 0.001
## 42    WAVI  0.61917664  0.0134397815 0.001
## 43    WBNU -0.49381593 -0.2739331013 0.001
## 44    WIFL  0.47094574  0.0004034451 0.001
## 45    WOTH -0.31895854 -0.3625536846 0.001
## 46    YEWA  0.71017760 -0.0122296428 0.001
## 47    YTVI -0.28821198 -0.2674515592 0.001

47 species were identified as significantly contributing to variation between plots. These are my best attempts to break these down by typical migratory patterns for each species in Ohio (courtesy of www.allaboutbirds.org).

Neotropical migrants: Acadian Fly-Catcher, Baltimore Oriole, Barn Swallow, Common Yellowthroat, Eastern Kingbird, Eastern Wood-Pewee, Great Crested Flycatcher, Hooded Warbler, Indigo Bunting, Orchard Oriole, Rose-Breasted Grosbeak, Red-Eyed Vireo, Scarlet Tanager, Warbling Vireo, Willow Flycatcher, Wood Thrush, Yellow Warbler, Yellow-Throated Vireo = 18 species

Resident: American Crow, American Kestrel, European Starling, Hairy Woodpecker, House Sparrow, Pileated Woodpecker, Song Sparrow, White-Breasted Nuthatch = 8 species

Short-distance migrant: American Goldfinch, Black-capped Chickadee, Blue-Gray Gnatcatcher, Brown-headed Cowbird, Brown Thrasher, Cedar Waxwing, Common Grackle, Eastern Bluebird, Eastern Meadowlark, Field Sparrow, Gray Catbird, House Wren, Killdeer, Mourning Dove, Northern Flicker, Northern Rough-winged Swallow, Red-winged Blackbird, Tree Swallow, Turkey Vulture = 19 species

Resident or migratory: Canada Goose, Dark-eyed Junco = 2 species

We can repeat this procedure for the PCOA results too. Whereas PCA (above) was based on summarizing our bird community in the fewest number of axes that explain the most variance, PCOA is trying to maximize distance between plots. This is somewhat semantic in many cases, but will lead to differing representations of which birds are most associated with ordination axes.

Anyway! on to the PCOA:

##    species         MDS1        MDS2 pvals
## 1     ACFL -0.731621770 -0.21657507 0.001
## 2     AMRO  0.212185897  0.26237816 0.001
## 3     BAOR  0.496278108 -0.11707782 0.001
## 4     BARS  0.396414060 -0.14525664 0.001
## 5     BGGN -0.253771660 -0.21321227 0.001
## 6     BHCO  0.252189128 -0.33826670 0.001
## 7     BRTH  0.332695547 -0.17755430 0.001
## 8     CEDW  0.528291870 -0.15714239 0.001
## 9     CHSW -0.008700066 -0.32221685 0.001
## 10    COGR  0.449821060  0.15723190 0.001
## 11    COYE  0.516757753 -0.36308017 0.001
## 12    DEJU -0.353475491 -0.17838667 0.001
## 13    EAKI  0.323351441 -0.09112853 0.001
## 14    EATO  0.130826116 -0.28201583 0.001
## 15    EAWP -0.531425079 -0.06810441 0.001
## 16    EUST  0.564199285  0.00876616 0.001
## 17    FISP  0.247783137 -0.21620323 0.001
## 18    GRCA  0.606185199 -0.08760151 0.001
## 19    HAWO -0.240271017 -0.22737147 0.001
## 20    HOFI  0.344663351  0.14118008 0.001
## 21    HOSP  0.357013239  0.15621096 0.001
## 22    HOWA -0.446954750 -0.49945770 0.001
## 23    HOWR  0.363416944  0.14393149 0.001
## 24    INBU  0.358710671 -0.48692796 0.001
## 25    LOWA -0.216453442 -0.34516208 0.001
## 26    MODO  0.503095502 -0.13966980 0.001
## 27    NOFL  0.338135730 -0.04580320 0.001
## 28    NRWS  0.299804802 -0.05498756 0.001
## 29    OROR  0.635092702 -0.04190854 0.001
## 30    OVEN -0.178146781 -0.19698291 0.001
## 31    PIWO -0.211414515 -0.44190745 0.001
## 32    RBGR  0.335449325 -0.27805077 0.001
## 33    REVI -0.427474339 -0.05322856 0.001
## 34    RWBL  0.659017118 -0.04422247 0.001
## 35    SCTA -0.563727972 -0.35767304 0.001
## 36    SOSP  0.654370712 -0.10449673 0.001
## 37    TRES  0.446180461 -0.04558460 0.001
## 38    VEER -0.141621359 -0.32912045 0.001
## 39    WAVI  0.590289204  0.02894698 0.001
## 40    WBNU -0.423708109 -0.15390376 0.001
## 41    WIFL  0.417164492 -0.19105681 0.001
## 42    WOTH -0.273041942 -0.51805873 0.001
## 43    YEWA  0.695495064 -0.12652046 0.001
## 44    YTVI -0.257925903 -0.31119268 0.001

So, now we have 44 species that contribute most to community distance between plots.

Neotropical migrants: Acadian Fly-Catcher, Baltimore Oriole, Barn Swallow, Chimney Swift, Common Yellowthroat, Eastern Kingbird, Eastern Wood-Pewee, Hooded Warbler, Indigo Bunting, Louisiana Water-Thrush, Orchard Oriole, Ovenbird, Rose-Breasted Grosbeak, Red-Eyed Vireo, Scarlet Tanager, Veery, Warbling Vireo, Willow Flycatcher, Wood Thrush, Yellow Warbler, Yellow-Throated Vireo = 21 species

Resident: European Starling, Hairy Woodpecker, House Finch, House Sparrow, Pileated Woodpecker, Song Sparrow, White-Breasted Nuthatch = 7 species

Short-distance migrant: American Robin, Blue-Gray Gnatcatcher, Brown-headed Cowbird, Brown Thrasher, Cedar Waxwing, Common Grackle, Eastern Towhee, Field Sparrow, Gray Catbird, House Wren, Mourning Dove, Northern Flicker, Northern Rough-winged Swallow, Red-winged Blackbird, Tree Swallow = 15 species

Resident or migratory: Dark-eyed Junco = 1 species

and now the NMDS:

##    species      NMDS1        NMDS2 pvals
## 1     ACFL -0.6618348 -0.341392498 0.001
## 2     AMCR -0.1809373 -0.228515977 0.001
## 3     AMRO  0.1629920  0.302705875 0.001
## 4     BAOR  0.4772962 -0.127988404 0.001
## 5     BARS  0.3860442 -0.157950082 0.001
## 6     BCCH -0.1840405 -0.247342387 0.001
## 7     BGGN -0.1661447 -0.310696158 0.001
## 8     BHCO  0.2053812 -0.323500671 0.001
## 9     BRTH  0.2829251 -0.255309288 0.001
## 10    CEDW  0.4945065 -0.161253661 0.001
## 11    COGR  0.4097261  0.223524723 0.001
## 12    COYE  0.4294219 -0.454069222 0.001
## 13    DEJU -0.2800585 -0.283832953 0.001
## 14    EAKI  0.3026501 -0.153678817 0.001
## 15    EAWP -0.5238803 -0.171371275 0.001
## 16    EUST  0.5579432  0.034119785 0.001
## 17    FISP  0.1842373 -0.297461046 0.001
## 18    GRCA  0.5913728  0.010163788 0.001
## 19    HOFI  0.2689176  0.261298811 0.001
## 20    HOSP  0.2863387  0.281273735 0.001
## 21    HOWA -0.3076686 -0.569869867 0.001
## 22    HOWR  0.3001183  0.252110188 0.001
## 23    INBU  0.2709295 -0.507591667 0.001
## 24    LOWA -0.1380231 -0.364701465 0.001
## 25    MODO  0.4666425 -0.213629459 0.001
## 26    NOFL  0.3201925  0.012743833 0.001
## 27    OROR  0.6399450 -0.052994011 0.001
## 28    PIWO -0.1194412 -0.400313818 0.001
## 29    RBGR  0.2673543 -0.328081328 0.001
## 30    REVI -0.4342023 -0.084154867 0.001
## 31    RWBL  0.6464910 -0.020637450 0.001
## 32    SCTA -0.4227056 -0.474345456 0.001
## 33    SOSP  0.6408078 -0.111264386 0.001
## 34    TRES  0.4323321 -0.091271373 0.001
## 35    WAVI  0.5938069 -0.002640012 0.001
## 36    WBNU -0.3459764 -0.293921549 0.001
## 37    WIFL  0.3889553 -0.241823500 0.001
## 38    WOTH -0.1553185 -0.520658575 0.001
## 39    YEWA  0.6794610 -0.197506714 0.001
## 40    YTVI -0.1666356 -0.363636777 0.001

So, now we have 40 species that contribute most to community distance between plots.

Neotropical migrants: Acadian Fly-Catcher, Baltimore Oriole, Barn Swallow, Common Yellowthroat, Eastern Kingbird, Eastern Wood-Pewee, Hooded Warbler, Indigo Bunting, Louisiana Water-Thrush, Orchard Oriole, Rose-Breasted Grosbeak, Red-Eyed Vireo, Scarlet Tanager, Warbling Vireo, Willow Flycatcher, Wood Thrush, Yellow Warbler, Yellow-Throated Vireo = 18 species

Resident: American Crow, European Starling, House Finch, House Sparrow, Pileated Woodpecker, Song Sparrow, White-Breasted Nuthatch = 7 species

Short-distance migrant: American Robin, Black-Capped Chickadee, Blue-Gray Gnatcatcher, Brown-headed Cowbird, Brown Thrasher, Cedar Waxwing, Common Grackle, Field Sparrow, Gray Catbird, House Wren, Mourning Dove, Northern Flicker, Red-winged Blackbird, Tree Swallow = 14 species

Resident or migratory: Dark-eyed Junco = 1 species

While these three sets of species are pretty similar, we can also take a look at which species are different across approaches.

outersect(fit_spp$species,fit_pcoa_spp$species,fitpca_spp$species)
##  [1] "CHSW" "EATO" "OVEN" "VEER" "AMGO" "AMKE" "CANG" "EABL" "EAME" "GCFL" "KILL" "TUVU"

So American Goldfinch, American Kestrel, Canada Goose, Chimney Swift, Eastern Bluebird, Eastern Meadowlark, Easter Towhee, Great-Crested Flycatcher, Killdeer, Ovenbird, Tufted Titmouse, Turkey Vulture, and Veery. At least to me, nothing particularly sticks out as a commonality across these species, but it may make just as much sense to simply pool these species across approaches:

sort(unique(c(fit_spp$species,fit_pcoa_spp$species,fitpca_spp$species)))
##  [1] "ACFL" "AMCR" "AMGO" "AMKE" "AMRO" "BAOR" "BARS" "BCCH" "BGGN" "BHCO" "BRTH" "CANG" "CEDW" "CHSW" "COGR" "COYE" "DEJU" "EABL" "EAKI" "EAME" "EATO" "EAWP" "EUST" "FISP" "GCFL" "GRCA" "HAWO" "HOFI" "HOSP" "HOWA" "HOWR" "INBU" "KILL" "LOWA" "MODO" "NOFL" "NRWS" "OROR" "OVEN" "PIWO" "RBGR" "REVI" "RWBL" "SCTA" "SOSP" "TRES" "TUVU" "VEER" "WAVI" "WBNU" "WIFL" "WOTH" "YEWA" "YTVI"

This gives us a list of 54 bird species that seem to be particularly differentiated/variable across plots. That is about half of the total number of species in the overall dataset.

As we proceed, we will begin layering on our environmental datasets using three main approaches: constrained ordination, linear models of species richness, and multi-species occupancy models.

constrained

Whereas the ordination approaches above were focused on unconstrained ordination - in this case, exploring how species are arranged between sample sites - there is an entire suite of approaches that address how environmental gradients shape community assemblages among sample sites. These are called constrained ordination approaches. I am personally a huge proponent of redundancy analysis (RDA) as a flexible constrained ordination approach. Taken from the GUSTA ME tutorial on RDA:

RDA can also be considered a constrained version of principal components analysis (PCA), wherein canonical axes - built from linear combinations of response variables - must also be linear combinations of the explanatory variables (i.e. fitted by [multiple linear regression]). The RDA approach generates one ordination in the space defined by the matrix of response variables and another in the space defined by the matrix of explanatory variables.

So, in essence, the ordination plot produced will depict an optimal arrangement of environmental axes (RDA1, 2, etc.) that maximally explains variation in the species dataset.

We are going to use stepwise selection to explore which PCAP covariates most explain plot-level differences.

p<-rda(birdcomm_bin~.,vegecomm_drop,scale=T)
fit<-envfit(p,vegecomm_drop,scale=T)


p_0<-rda(birdcomm_bin~1,vegecomm_drop,scale=T)
p_1<-rda(birdcomm_bin~.,vegecomm_drop,scale=T)

set.seed(12345)
p_step<- ordistep(p_0, scope = formula(p_1))
## 
## Start: birdcomm_bin ~ 1 
## 
##                   Df    AIC      F Pr(>F)   
## + tol_rel          1 756.52 6.6278  0.005 **
## + svp              1 759.75 3.3367  0.005 **
## + sens_rel         1 760.08 3.0040  0.005 **
## + bryo             1 760.13 2.9488  0.005 **
## + shrub            1 760.69 2.3887  0.005 **
## + dicot            1 760.69 2.3868  0.005 **
## + sens_rel_notree  1 760.88 2.2021  0.005 **
## + cyper            1 761.26 1.8240  0.005 **
## + canopy           1 761.40 1.6763  0.005 **
## + subcanopy        1 761.12 1.9604  0.010 **
## + inv              1 760.60 2.4803  0.060 . 
## + hydro            1 761.74 1.3427  0.100 . 
## + small_tree       1 761.92 1.1632  0.170   
## + hydro_rel        1 761.99 1.0958  0.275   
## + ap               1 762.20 0.8798  0.540   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel 
## 
##           Df    AIC      F Pr(>F)   
## - tol_rel  1 761.09 6.6278  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                   Df    AIC      F Pr(>F)   
## + dicot            1 756.24 2.2478  0.005 **
## + svp              1 756.39 2.1026  0.005 **
## + cyper            1 756.71 1.7803  0.005 **
## + shrub            1 757.07 1.4294  0.040 * 
## + hydro            1 757.10 1.3944  0.045 * 
## + canopy           1 757.20 1.2963  0.055 . 
## + bryo             1 757.00 1.4934  0.075 . 
## + inv              1 756.58 1.9137  0.080 . 
## + small_tree       1 757.34 1.1623  0.190   
## + subcanopy        1 757.40 1.0978  0.300   
## + hydro_rel        1 757.45 1.0499  0.340   
## + sens_rel_notree  1 757.44 1.0559  0.365   
## + sens_rel         1 757.47 1.0350  0.365   
## + ap               1 757.67 0.8305  0.630   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + dicot 
## 
##           Df    AIC      F Pr(>F)   
## - dicot    1 756.52 2.2478  0.005 **
## - tol_rel  1 760.69 6.4593  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                   Df    AIC      F Pr(>F)   
## + cyper            1 756.25 1.9574  0.005 **
## + svp              1 756.27 1.9327  0.005 **
## + bryo             1 756.70 1.5120  0.075 . 
## + canopy           1 756.91 1.3088  0.080 . 
## + inv              1 756.29 1.9117  0.090 . 
## + small_tree       1 757.04 1.1759  0.170   
## + shrub            1 757.12 1.0959  0.270   
## + subcanopy        1 757.16 1.0578  0.310   
## + sens_rel_notree  1 757.16 1.0562  0.330   
## + sens_rel         1 757.17 1.0523  0.360   
## + hydro_rel        1 757.21 1.0153  0.395   
## + ap               1 757.38 0.8394  0.575   
## + hydro            1 757.31 0.9108  0.690   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + dicot + cyper 
## 
##           Df    AIC      F Pr(>F)   
## - cyper    1 756.24 1.9574  0.005 **
## - dicot    1 756.71 2.4225  0.005 **
## - tol_rel  1 760.77 6.4911  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                   Df    AIC      F Pr(>F)   
## + svp              1 756.38 1.8188  0.005 **
## + bryo             1 756.65 1.5586  0.055 . 
## + inv              1 756.28 1.9242  0.085 . 
## + canopy           1 756.94 1.2725  0.115   
## + small_tree       1 757.02 1.1915  0.180   
## + shrub            1 757.07 1.1488  0.220   
## + sens_rel_notree  1 757.13 1.0914  0.315   
## + subcanopy        1 757.15 1.0663  0.330   
## + hydro_rel        1 757.19 1.0333  0.330   
## + sens_rel         1 757.16 1.0628  0.370   
## + hydro            1 757.31 0.9137  0.675   
## + ap               1 757.51 0.7199  0.810   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + dicot + cyper + svp 
## 
##           Df    AIC      F Pr(>F)   
## - cyper    1 756.27 1.8433  0.010 **
## - svp      1 756.25 1.8188  0.005 **
## - dicot    1 756.85 2.4083  0.005 **
## - tol_rel  1 759.89 5.4262  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                   Df    AIC      F Pr(>F)  
## + canopy           1 757.06 1.2840  0.070 .
## + inv              1 756.38 1.9384  0.080 .
## + bryo             1 757.00 1.3349  0.085 .
## + small_tree       1 757.21 1.1334  0.275  
## + shrub            1 757.29 1.0554  0.330  
## + hydro_rel        1 757.30 1.0438  0.395  
## + sens_rel_notree  1 757.32 1.0276  0.400  
## + subcanopy        1 757.32 1.0316  0.405  
## + sens_rel         1 757.37 0.9791  0.515  
## + hydro            1 757.43 0.9184  0.600  
## + ap               1 757.62 0.7415  0.785  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
p_step
## Call: rda(formula = birdcomm_bin ~ tol_rel + dicot + cyper + svp, data = vegecomm_drop, scale = T)
## 
##                 Inertia Proportion Rank
## Total         103.00000    1.00000     
## Constrained     7.68058    0.07457    4
## Unconstrained  95.31942    0.92543  102
## Inertia is correlations 
## 
## Eigenvalues for constrained axes:
##  RDA1  RDA2  RDA3  RDA4 
## 4.484 1.491 0.984 0.721 
## 
## Eigenvalues for unconstrained axes:
##   PC1   PC2   PC3   PC4   PC5   PC6   PC7   PC8 
## 6.460 3.678 3.582 3.215 3.037 2.621 2.553 2.371 
## (Showing 8 of 102 unconstrained eigenvalues)
anova(p_step)
## Permutation test for rda under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + dicot + cyper + svp, data = vegecomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## Model      4    7.681 3.2029  0.001 ***
## Residual 159   95.319                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_step,by="term")
## Permutation test for rda under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + dicot + cyper + svp, data = vegecomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## tol_rel    1    4.048 6.7529  0.001 ***
## dicot      1    1.362 2.2727  0.001 ***
## cyper      1    1.179 1.9674  0.002 ** 
## svp        1    1.090 1.8188  0.004 ** 
## Residual 159   95.319                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_step,by="axis")
## Permutation test for rda under reduced model
## Forward tests for axes
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + dicot + cyper + svp, data = vegecomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## RDA1       1    4.484 7.4791  0.001 ***
## RDA2       1    1.491 2.4876  0.001 ***
## RDA3       1    0.984 1.6421  0.007 ** 
## RDA4       1    0.721 1.2030  0.120    
## Residual 159   95.319                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
pcapplot<-ordiplot(p_step,scaling=3,type="n")
points(pcapplot, "sites",pch=3, col=colpal_reserv[reserv])

ordihull(pcapplot,groups = reserv, col=colpal_reserv, lwd=3)
title("PCA (vegan rda version)")
legend(x="right", legend=levels(reserv), col=colpal_reserv,pch = 3,cex=0.5)

ggord(p_step,  xlim=c(-1.25,1),ylim = c(-0.5, 1),txt=4,arrow=TRUE,ptslab=TRUE,addsize=3, size =4,addcol = color_resid)

So this tells us that the most explanatory group of PCAP covariates is relative cover of tolerant plants (tol_rel), cover of dicots, cover of seedless vascular plants (svp), and cover of sedges (cyper). Rather conveniently, the relative cover of dicots, seedless vascular plants, and sedges is negatively associated with the relative cover of tolerant plant species.

As a quick caveat, these four variables only explain about 7.3% of the variation, as seen here (red is our environmental axes, black is our unconstrained axes):

constrained_eig <- p_step$CCA$eig/p_step$tot.chi*100
unconstrained_eig <- p_step$CA$eig/p_step$tot.chi*100
expl_var <- c(constrained_eig, unconstrained_eig)
barplot (expl_var[1:20], col = c(rep ('red', length (constrained_eig)), rep ('black', length (unconstrained_eig))),
         las = 2, ylab = '% variation')

This is not that terribly uncommon for redundancy analyses - It is often difficult to find environmental gradients that explain all of the variance in large datasets like ours. Biologically, we likely do not necessarily expect that a single environmental gradient alone drives all of the variation in bird presence/absence, and intuitively know that we also have to worry about observer effects, weather, and other unmeasured characteristics. Regardless of any of the above, the ordination is significant - as are the relationships with these covariates, so we can safely say that nearly 10% of the variation in our bird species dataset is explainable by these 4 PCAP covariates!

We can also explore just the landscape covariate associations:

p_land<-rda(birdcomm_bin~.,landcomm_drop,scale=T)
fit<-envfit(p_land,landcomm_drop,scale=T)


p_land_0<-rda(birdcomm_bin~1,landcomm_drop,scale=T)
p_land_1<-rda(birdcomm_bin~.,landcomm_drop,scale=T)

set.seed(12345)
p_land_step<- ordistep(p_land_0, scope = formula(p_land_1))
## 
## Start: birdcomm_bin ~ 1 
## 
##                    Df    AIC      F Pr(>F)   
## + ldi.index.score   1 757.95 5.1630  0.005 **
## + developed         1 758.98 4.1092  0.005 **
## + developed.edge    1 759.84 3.2411  0.005 **
## + activity.area     1 761.16 1.9193  0.005 **
## + stream.edge       1 761.88 1.2024  0.110   
## + bootleg.trail     1 762.09 0.9947  0.450   
## + sanctioned.trail  1 762.29 0.7966  0.675   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ ldi.index.score 
## 
##                   Df    AIC     F Pr(>F)   
## - ldi.index.score  1 761.09 5.163  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + developed         1 757.14 2.7814  0.005 **
## + developed.edge    1 757.95 1.9718  0.005 **
## + activity.area     1 758.44 1.4863  0.030 * 
## + bootleg.trail     1 758.99 0.9469  0.570   
## + stream.edge       1 759.03 0.9043  0.685   
## + sanctioned.trail  1 759.14 0.7908  0.745   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ ldi.index.score + developed 
## 
##                   Df    AIC      F Pr(>F)   
## - developed        1 757.95 2.7814  0.005 **
## - ldi.index.score  1 758.98 3.8205  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)  
## + developed.edge    1 757.60 1.5110  0.025 *
## + activity.area     1 757.87 1.2450  0.130  
## + bootleg.trail     1 758.15 0.9660  0.490  
## + stream.edge       1 758.15 0.9697  0.560  
## + sanctioned.trail  1 758.33 0.7943  0.745  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ ldi.index.score + developed + developed.edge 
## 
##                   Df    AIC      F Pr(>F)   
## - developed.edge   1 757.14 1.5110  0.015 * 
## - developed        1 757.95 2.3133  0.005 **
## - ldi.index.score  1 758.95 3.3091  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)
## + activity.area     1 758.36 1.2015  0.155
## + bootleg.trail     1 758.60 0.9735  0.455
## + stream.edge       1 758.61 0.9637  0.550
## + sanctioned.trail  1 758.72 0.8503  0.690
p_land_step
## Call: rda(formula = birdcomm_bin ~ ldi.index.score + developed + developed.edge, data = landcomm_drop, scale = T)
## 
##                 Inertia Proportion Rank
## Total         103.00000    1.00000     
## Constrained     5.79442    0.05626    3
## Unconstrained  97.20558    0.94374  102
## Inertia is correlations 
## 
## Eigenvalues for constrained axes:
##  RDA1  RDA2  RDA3 
## 4.002 1.157 0.636 
## 
## Eigenvalues for unconstrained axes:
##   PC1   PC2   PC3   PC4   PC5   PC6   PC7   PC8 
## 7.848 3.913 3.573 3.413 2.734 2.620 2.498 2.444 
## (Showing 8 of 102 unconstrained eigenvalues)
anova(p_land_step)
## Permutation test for rda under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ ldi.index.score + developed + developed.edge, data = landcomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## Model      3    5.794 3.1792  0.001 ***
## Residual 160   97.206                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_land_step,by="term")
## Permutation test for rda under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ ldi.index.score + developed + developed.edge, data = landcomm_drop, scale = T)
##                  Df Variance      F Pr(>F)    
## ldi.index.score   1    3.181 5.2364  0.001 ***
## developed         1    1.695 2.7902  0.001 ***
## developed.edge    1    0.918 1.5110  0.020 *  
## Residual        160   97.206                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_land_step,by="axis")
## Permutation test for rda under reduced model
## Forward tests for axes
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ ldi.index.score + developed + developed.edge, data = landcomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## RDA1       1    4.002 6.5872  0.001 ***
## RDA2       1    1.157 1.9039  0.007 ** 
## RDA3       1    0.636 1.0464  0.370    
## Residual 160   97.206                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
ordiplot(p_land_step,scaling=3)

constrained_eig <- p_land_step$CCA$eig/p_land_step$tot.chi*100
unconstrained_eig <- p_land_step$CA$eig/p_land_step$tot.chi*100
expl_var <- c(constrained_eig, unconstrained_eig)
barplot (expl_var[1:20], col = c(rep ('red', length (constrained_eig)), rep ('black', length (unconstrained_eig))),
         las = 2, ylab = '% variation')

And now for the vegetation and land cover dataset:

p_landveg<-rda(birdcomm_bin~.,landvegcomm_drop,scale=T)
fit_landveg<-envfit(p_landveg,landvegcomm_drop,scale=T)


p_landveg_0<-rda(birdcomm_bin~1,landvegcomm_drop,scale=T)
p_landveg_1<-rda(birdcomm_bin~.,landvegcomm_drop,scale=T)

set.seed(12345)
p_landveg_step<- ordistep(p_landveg_0, scope = formula(p_landveg_1))
## 
## Start: birdcomm_bin ~ 1 
## 
##                    Df    AIC      F Pr(>F)   
## + tol_rel           1 756.52 6.6278  0.005 **
## + ldi.index.score   1 757.95 5.1630  0.005 **
## + developed         1 758.98 4.1092  0.005 **
## + svp               1 759.75 3.3367  0.005 **
## + developed.edge    1 759.84 3.2411  0.005 **
## + sens_rel          1 760.08 3.0040  0.005 **
## + bryo              1 760.13 2.9488  0.005 **
## + shrub             1 760.69 2.3887  0.005 **
## + dicot             1 760.69 2.3868  0.005 **
## + sens_rel_notree   1 760.88 2.2021  0.005 **
## + activity.area     1 761.16 1.9193  0.005 **
## + cyper             1 761.26 1.8240  0.005 **
## + canopy            1 761.40 1.6763  0.005 **
## + subcanopy         1 761.12 1.9604  0.010 **
## + inv               1 760.60 2.4803  0.060 . 
## + hydro             1 761.74 1.3427  0.100 . 
## + stream.edge       1 761.88 1.2024  0.140   
## + small_tree        1 761.92 1.1632  0.170   
## + hydro_rel         1 761.99 1.0958  0.275   
## + bootleg.trail     1 762.09 0.9947  0.480   
## + ap                1 762.20 0.8798  0.540   
## + sanctioned.trail  1 762.29 0.7966  0.775   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel 
## 
##           Df    AIC      F Pr(>F)   
## - tol_rel  1 761.09 6.6278  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + ldi.index.score   1 755.07 3.4193  0.005 **
## + developed         1 755.58 2.9108  0.005 **
## + developed.edge    1 756.09 2.3958  0.005 **
## + dicot             1 756.24 2.2478  0.005 **
## + svp               1 756.39 2.1026  0.005 **
## + cyper             1 756.71 1.7803  0.005 **
## + shrub             1 757.07 1.4294  0.030 * 
## + hydro             1 757.10 1.3944  0.060 . 
## + bryo              1 757.00 1.4934  0.070 . 
## + activity.area     1 757.22 1.2770  0.075 . 
## + canopy            1 757.20 1.2963  0.110   
## + inv               1 756.58 1.9137  0.115   
## + small_tree        1 757.34 1.1623  0.200   
## + subcanopy         1 757.40 1.0978  0.250   
## + hydro_rel         1 757.45 1.0499  0.310   
## + sens_rel_notree   1 757.44 1.0559  0.340   
## + sens_rel          1 757.47 1.0350  0.410   
## + stream.edge       1 757.48 1.0214  0.450   
## + bootleg.trail     1 757.55 0.9469  0.555   
## + ap                1 757.67 0.8305  0.565   
## + sanctioned.trail  1 757.75 0.7554  0.815   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score 
## 
##                   Df    AIC      F Pr(>F)   
## - ldi.index.score  1 756.52 3.4193  0.005 **
## - tol_rel          1 757.95 4.8600  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + developed         1 754.63 2.3992  0.005 **
## + dicot             1 755.06 1.9772  0.005 **
## + developed.edge    1 755.22 1.8181  0.005 **
## + svp               1 755.39 1.6498  0.015 * 
## + cyper             1 755.63 1.4137  0.020 * 
## + bryo              1 755.42 1.6202  0.035 * 
## + hydro             1 755.73 1.3160  0.060 . 
## + inv               1 755.05 1.9852  0.105   
## + canopy            1 755.82 1.2230  0.135   
## + shrub             1 755.85 1.1938  0.160   
## + small_tree        1 755.86 1.1833  0.160   
## + activity.area     1 755.83 1.2179  0.185   
## + sens_rel_notree   1 755.99 1.0566  0.305   
## + sens_rel          1 755.98 1.0659  0.335   
## + hydro_rel         1 755.98 1.0622  0.345   
## + subcanopy         1 755.97 1.0814  0.390   
## + bootleg.trail     1 756.11 0.9383  0.530   
## + ap                1 756.20 0.8542  0.560   
## + stream.edge       1 756.10 0.9472  0.580   
## + sanctioned.trail  1 756.26 0.7932  0.725   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score + developed 
## 
##                   Df    AIC      F Pr(>F)   
## - developed        1 755.07 2.3992  0.005 **
## - ldi.index.score  1 755.58 2.9029  0.005 **
## - tol_rel          1 757.14 4.4602  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + dicot             1 754.66 1.9247  0.005 **
## + developed.edge    1 755.11 1.4776  0.010 **
## + cyper             1 755.16 1.4314  0.010 **
## + svp               1 755.10 1.4884  0.015 * 
## + bryo              1 754.99 1.5955  0.055 . 
## + hydro             1 755.26 1.3298  0.055 . 
## + inv               1 754.59 1.9919  0.075 . 
## + shrub             1 755.34 1.2545  0.080 . 
## + small_tree        1 755.40 1.1947  0.110   
## + canopy            1 755.38 1.2126  0.140   
## + activity.area     1 755.49 1.1112  0.230   
## + hydro_rel         1 755.53 1.0710  0.250   
## + subcanopy         1 755.45 1.1442  0.270   
## + sens_rel          1 755.54 1.0568  0.275   
## + stream.edge       1 755.58 1.0209  0.440   
## + sens_rel_notree   1 755.61 0.9943  0.445   
## + bootleg.trail     1 755.65 0.9505  0.540   
## + ap                1 755.74 0.8626  0.560   
## + sanctioned.trail  1 755.81 0.8001  0.770   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot 
## 
##                   Df    AIC      F Pr(>F)   
## - dicot            1 754.63 1.9247  0.005 **
## - developed        1 755.06 2.3438  0.005 **
## - ldi.index.score  1 755.47 2.7566  0.005 **
## - tol_rel          1 757.22 4.4866  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + cyper             1 754.80 1.7982  0.005 **
## + svp               1 754.97 1.6335  0.015 * 
## + developed.edge    1 755.14 1.4698  0.020 * 
## + bryo              1 755.02 1.5865  0.040 * 
## + inv               1 754.63 1.9591  0.080 . 
## + canopy            1 755.38 1.2329  0.125   
## + small_tree        1 755.43 1.1879  0.170   
## + subcanopy         1 755.50 1.1216  0.200   
## + shrub             1 755.52 1.1028  0.265   
## + activity.area     1 755.52 1.1003  0.295   
## + sens_rel_notree   1 755.59 1.0274  0.345   
## + stream.edge       1 755.61 1.0084  0.380   
## + sens_rel          1 755.57 1.0473  0.385   
## + hydro_rel         1 755.59 1.0263  0.385   
## + bootleg.trail     1 755.67 0.9571  0.495   
## + ap                1 755.74 0.8843  0.505   
## + hydro             1 755.69 0.9316  0.615   
## + sanctioned.trail  1 755.83 0.7992  0.740   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot +      cyper 
## 
##                   Df    AIC      F Pr(>F)   
## - cyper            1 754.66 1.7982  0.005 **
## - dicot            1 755.16 2.2896  0.005 **
## - developed        1 755.22 2.3523  0.005 **
## - ldi.index.score  1 755.44 2.5658  0.005 **
## - tol_rel          1 757.43 4.5207  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + svp               1 755.18 1.5626  0.005 **
## + developed.edge    1 755.27 1.4705  0.005 **
## + bryo              1 755.11 1.6223  0.055 . 
## + inv               1 754.77 1.9510  0.065 . 
## + small_tree        1 755.53 1.2174  0.120   
## + canopy            1 755.53 1.2202  0.150   
## + shrub             1 755.61 1.1465  0.205   
## + activity.area     1 755.64 1.1154  0.245   
## + subcanopy         1 755.62 1.1296  0.255   
## + sens_rel          1 755.70 1.0548  0.275   
## + sens_rel_notree   1 755.70 1.0570  0.350   
## + hydro_rel         1 755.72 1.0380  0.395   
## + stream.edge       1 755.74 1.0187  0.465   
## + bootleg.trail     1 755.80 0.9623  0.505   
## + hydro             1 755.83 0.9311  0.620   
## + ap                1 756.01 0.7564  0.740   
## + sanctioned.trail  1 755.97 0.7935  0.765   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot +      cyper + svp 
## 
##                   Df    AIC      F Pr(>F)   
## - svp              1 754.80 1.5626  0.020 * 
## - cyper            1 754.97 1.7262  0.015 * 
## - developed        1 755.51 2.2513  0.005 **
## - dicot            1 755.70 2.4307  0.005 **
## - ldi.index.score  1 755.76 2.4944  0.005 **
## - tol_rel          1 757.47 4.1679  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)   
## + developed.edge    1 755.63 1.4782  0.010 **
## + bryo              1 755.68 1.4287  0.075 . 
## + inv               1 755.13 1.9606  0.095 . 
## + canopy            1 755.90 1.2140  0.100 . 
## + small_tree        1 756.00 1.1225  0.245   
## + subcanopy         1 756.04 1.0809  0.275   
## + shrub             1 756.05 1.0746  0.305   
## + hydro_rel         1 756.08 1.0451  0.320   
## + activity.area     1 756.02 1.1077  0.325   
## + stream.edge       1 756.10 1.0230  0.380   
## + sens_rel_notree   1 756.11 1.0199  0.450   
## + sens_rel          1 756.14 0.9925  0.485   
## + bootleg.trail     1 756.16 0.9663  0.490   
## + hydro             1 756.20 0.9339  0.580   
## + sanctioned.trail  1 756.34 0.8010  0.735   
## + ap                1 756.36 0.7785  0.750   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Step: birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot +      cyper + svp + developed.edge 
## 
##                   Df    AIC      F Pr(>F)   
## - developed.edge   1 755.18 1.4782  0.040 * 
## - developed        1 755.67 1.9493  0.015 * 
## - svp              1 755.27 1.5697  0.005 **
## - cyper            1 755.43 1.7273  0.005 **
## - ldi.index.score  1 756.08 2.3485  0.005 **
## - dicot            1 756.18 2.4474  0.005 **
## - tol_rel          1 757.92 4.1336  0.005 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                    Df    AIC      F Pr(>F)  
## + inv               1 755.59 1.9361  0.080 .
## + bryo              1 756.06 1.4901  0.095 .
## + canopy            1 756.32 1.2376  0.120  
## + shrub             1 756.47 1.1019  0.285  
## + small_tree        1 756.47 1.1010  0.295  
## + subcanopy         1 756.47 1.0960  0.305  
## + activity.area     1 756.47 1.0971  0.310  
## + sens_rel_notree   1 756.51 1.0596  0.350  
## + bootleg.trail     1 756.59 0.9809  0.470  
## + hydro_rel         1 756.59 0.9877  0.475  
## + sens_rel          1 756.57 1.0067  0.500  
## + stream.edge       1 756.58 0.9954  0.510  
## + sanctioned.trail  1 756.72 0.8573  0.665  
## + hydro             1 756.68 0.8983  0.685  
## + ap                1 756.80 0.7809  0.705  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
p_landveg_step
## Call: rda(formula = birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot + cyper + svp + developed.edge, data = landvegcomm_drop, scale = T)
## 
##                Inertia Proportion Rank
## Total         103.0000     1.0000     
## Constrained    11.5265     0.1119    7
## Unconstrained  91.4735     0.8881  102
## Inertia is correlations 
## 
## Eigenvalues for constrained axes:
##  RDA1  RDA2  RDA3  RDA4  RDA5  RDA6  RDA7 
## 5.301 1.746 1.400 1.043 0.786 0.720 0.530 
## 
## Eigenvalues for unconstrained axes:
##   PC1   PC2   PC3   PC4   PC5   PC6   PC7   PC8 
## 6.002 3.613 3.427 3.157 2.615 2.495 2.438 2.353 
## (Showing 8 of 102 unconstrained eigenvalues)
anova(p_landveg_step)
## Permutation test for rda under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot + cyper + svp + developed.edge, data = landvegcomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## Model      7   11.527 2.8082  0.001 ***
## Residual 156   91.473                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_landveg_step,by="term")
## Permutation test for rda under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot + cyper + svp + developed.edge, data = landvegcomm_drop, scale = T)
##                  Df Variance      F Pr(>F)    
## tol_rel           1    4.048 6.9041  0.001 ***
## ldi.index.score   1    2.058 3.5094  0.001 ***
## developed         1    1.431 2.4412  0.003 ** 
## dicot             1    1.142 1.9471  0.002 ** 
## cyper             1    1.061 1.8101  0.002 ** 
## svp               1    0.919 1.5674  0.011 *  
## developed.edge    1    0.867 1.4782  0.024 *  
## Residual        156   91.473                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(p_landveg_step,by="axis")
## Permutation test for rda under reduced model
## Forward tests for axes
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = birdcomm_bin ~ tol_rel + ldi.index.score + developed + dicot + cyper + svp + developed.edge, data = landvegcomm_drop, scale = T)
##           Df Variance      F Pr(>F)    
## RDA1       1    5.301 9.0404  0.001 ***
## RDA2       1    1.746 2.9783  0.001 ***
## RDA3       1    1.400 2.3878  0.002 ** 
## RDA4       1    1.043 1.7781  0.022 *  
## RDA5       1    0.786 1.3413  0.305    
## RDA6       1    0.720 1.2273  0.307    
## RDA7       1    0.530 0.9043  0.689    
## Residual 156   91.473                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
ordiplot(p_landveg_step,scaling=3)

constrained_eig <- p_landveg_step$CCA$eig/p_landveg_step$tot.chi*100
unconstrained_eig <- p_landveg_step$CA$eig/p_landveg_step$tot.chi*100
expl_var <- c(constrained_eig, unconstrained_eig)
barplot (expl_var[1:20], col = c(rep ('red', length (constrained_eig)), rep ('black', length (unconstrained_eig))),
         las = 2, ylab = '% variation')

Some interesting things are going on here. RDA1 primarily captures both plot-scale and landscape-scale indicators of disturbance - namely, relative cover of tolerant plant species (plot level) and landscape disturbance index (at a landscape-level) contrasted with indicators of less disturbance - namely, further distances to developed land, more seedless vascular plants, more cyperaceae, and more dicots. This one axis explains upwards of 5% of variation - so we are doing pretty well in that regard. Across all seven axes, we are approaching about 11% explained variance. In addition, stepwise selection basically confirms variable selection for the land cover and vegetation datasets run separately - the same variables included in those best-supported model statements are in this full model.

We can also explore bird species most significantly associated with our constrained ordination axes, too. We will focus on the full (land cover and vegetation) ordination.

# envfit() takes the output of metaMDS() and the species matrix you created
fitconcrda <- envfit(p_step, birdcomm_bin, perm = 999) 

# extract p-values for each species
fitconcrda_pvals <- fitconcrda$vectors$pvals %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  dplyr::rename("pvals" = ".")

# extract coordinates for species, only keep species with p-val = 0.001
fitconcrda_spp <- fitconcrda %>% 
  scores(., display = "vectors") %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  full_join(., fitconcrda_pvals, by = "species") %>% 
  filter(pvals == 0.001)

OK - this is getting towards our main analytical goals! Let’s sort by scores for that first environmental axis and plot these in order:

BBSMigrants_sub_sig<-BBSMigrants_sub[BBSMigrants_sub$SpeciesCode %in% fitconcrda_spp$species,]

BBSMigrants_sub_sig_reorder<-BBSMigrants_sub_sig[order(BBSMigrants_sub_sig$SpeciesCode),]

fitconcrda_spp_reorder<-fitconcrda_spp[order(fitconcrda_spp$species),]

fitconcrda_spp_join<-cbind(fitconcrda_spp_reorder,BBSMigrants_sub_sig_reorder)


fitconcrda_spp_order<-fitconcrda_spp_join[order(fitconcrda_spp_join$RDA1),]
fitconcrda_spp_order$species<-factor(fitconcrda_spp_order$species,levels=fitconcrda_spp_order$species)

fitconcrda_spp_order$color_resid[fitconcrda_spp_order$Residency %in% "NE"]<-"blue"

fitconcrda_spp_order$color_resid[fitconcrda_spp_order$Residency %in% "M"]<-"green"

fitconcrda_spp_order$color_resid[fitconcrda_spp_order$Residency %in% "R"]<-"red"



color_sub<-fitconcrda_spp_order$color_resid

ggplot(aes(x=RDA1,y=species),data=fitconcrda_spp_order)+geom_point()+theme_classic(base_size=18)+theme(axis.text.y = element_text(colour = color_sub))
## Warning: Vectorized input to `element_text()` is not officially supported.
## Results may be unexpected or may change in future versions of ggplot2.

This is a pretty neat plot - Acadian Flycatcher, Scarlet Tanager, Eastern Wood-Pewee, White-breasted Nuthatch, Hooded Warbler, Red-Eyed Vireo, Dark-Eyed Junco, Wood Thrush, Hairy Woodpeckers, and Lousiana Water-Thrush all appear to be associated with higher sedge, seedless vascular plant, and dicot cover and lower cover of tolerant plants. In contrast, Yellow Warblers, Orchard Orioles, Red-Winged Blackbirds, European Starlings, Warbling Vireos, Song Sparrows, Grey Catbirds, Tree Swallows, Mourning Doves, and Cedar Waxwings are all associated with more tolerant plants. In addition, virtually all of our more tolerant vegetation-associated species are short-distance migrants, whereas the less tolerant vegetation-associated species are mostly neotropical migrants.

constrained - sites

While we have already explored environmental associations, we might also want to know what species are most differentiated between reservations. We will then use similar code to that used above to explore species that are most differentiated between reservations.

p_reservations<-rda(birdcomm_bin~reservatio,CMP_bbs_pcap_join_pcaponly_pcapsum,scale=T)

reservations_fitbirds<-envfit(p_reservations,birdcomm_bin)

reservations_fit<-envfit(p_reservations~reservatio,data=CMP_bbs_pcap_join_pcaponly_pcapsum,scale=T)


CMP_bbs_pcap_join_pcaponly_pcapsum$site<-rownames(CMP_bbs_pcap_join_pcaponly_pcapsum)

plot_df_reservations <- scores(p_reservations, display = "sites") %>% 
  as.data.frame() %>% 
  rownames_to_column("site") %>% 
  full_join(CMP_bbs_pcap_join_pcaponly_pcapsum, by = "site")

plot_rda_reservations <- ggplot(plot_df_reservations, aes(x = RDA1, y = RDA2, color = reservatio)) +
  geom_point(size = 3, alpha = 0.8) +
  stat_ellipse(linetype = 2, size = 1) +
  labs(title = "RDA")
plot_rda_reservations

fitreservations_pvals <- reservations_fitbirds$vectors$pvals %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  dplyr::rename("pvals" = ".")

# extract coordinates for species, only keep species with p-val = 0.001
fit_reservations_spp <- reservations_fitbirds %>% 
  scores(., display = "vectors") %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  full_join(., fitreservations_pvals, by = "species") %>% 
  filter(pvals == 0.001)
fit_reservations_spp
##    species        RDA1         RDA2 pvals
## 1     ACFL -0.66777571  0.117759129 0.001
## 2     AMCR -0.38752464 -0.218120450 0.001
## 3     AMKE  0.36069599  0.005207019 0.001
## 4     AMRE -0.11691782 -0.417572542 0.001
## 5     AMRO  0.26690627  0.242961322 0.001
## 6     BAOR  0.40912220  0.147084861 0.001
## 7     BARS  0.36426344 -0.297948461 0.001
## 8     BCCH -0.25654264  0.173591143 0.001
## 9     BRCR -0.28687748 -0.100539363 0.001
## 10    BRTH  0.24661825 -0.249101923 0.001
## 11    CEDW  0.40587243 -0.318529350 0.001
## 12    COGR  0.51500011  0.167583353 0.001
## 13    COYE  0.09667555 -0.532851862 0.001
## 14    DEJU -0.37639933 -0.016388874 0.001
## 15    EATO -0.13543382 -0.284272455 0.001
## 16    EAWP -0.46229095  0.436908082 0.001
## 17    EUST  0.54673983 -0.420762254 0.001
## 18    FISP -0.03106708 -0.366765924 0.001
## 19    GRCA  0.46354706 -0.107291445 0.001
## 20    HOFI  0.37928897 -0.073545643 0.001
## 21    HOSP  0.47178576  0.090612801 0.001
## 22    HOWA -0.57041850 -0.263142828 0.001
## 23    HOWR  0.31605596  0.122088141 0.001
## 24    INBU  0.14221796 -0.277445296 0.001
## 25    LOWA -0.30349510 -0.265588533 0.001
## 26    MALL  0.36539436  0.040174144 0.001
## 27    MODO  0.35803008 -0.169949443 0.001
## 28    NOFL  0.30190291  0.142456672 0.001
## 29    NRWS  0.44565648  0.077961759 0.001
## 30    OROR  0.53857451 -0.399968564 0.001
## 31    OVEN -0.32654527 -0.281863336 0.001
## 32    RBGU  0.36628682 -0.086059767 0.001
## 33    REVI -0.30390875  0.295754816 0.001
## 34    RWBL  0.50404846 -0.271167918 0.001
## 35    SCTA -0.54375433  0.062745434 0.001
## 36    SOSP  0.45897351 -0.181014710 0.001
## 37    TRES  0.44363253 -0.106280777 0.001
## 38    TUTI -0.28142388  0.201253917 0.001
## 39    TUVU  0.05394872 -0.299642895 0.001
## 40    VEER -0.25657805 -0.198795371 0.001
## 41    WAVI  0.54661431 -0.284150723 0.001
## 42    WBNU -0.47299945  0.272560858 0.001
## 43    WIFL  0.30162601 -0.294272609 0.001
## 44    WOTH -0.36226821 -0.032288378 0.001
## 45    YEWA  0.50814724 -0.424006710 0.001
## 46    YTVI -0.36532038 -0.235368151 0.001
fit_reservations <- reservations_fit %>% 
  scores(., display = "factors") %>% 
  as.data.frame() %>%
  rownames_to_column("reservations")

rda_reservation_plot_new <- ggplot(plot_df_reservations, aes(x = RDA1, y = RDA2)) +coord_fixed() +
  geom_point(aes(color = reservatio), size = 3, alpha = 0.8) +
  geom_segment(data = fit_reservations_spp, aes(x = 0, xend = RDA1, y = 0, yend = RDA2),col = "black") +
  geom_text(data = fit_reservations_spp, aes(label = species))+
  geom_text(data=as.data.frame(fit_reservations),aes(label=reservations))
rda_reservation_plot_new

Interesting! So when we consider reservation-of-origin, Hinckley seems to have a pretty unique bird community overall, and groups negatively along RDA1. In contrast, Brookside, Ohio and Erie Canal, and Washington all group positively along RDA1 - and are all quite heavily urbanized.

While I personally think the environmental gradient analyses are a bit more interesting, this does highlight reservations that are more or less distinct in bird community space. We can also plot just the reservations alone too:

ggplot(plot_df_reservations, aes(x = RDA1, y = RDA2)) +
  coord_fixed() +
  geom_text(data=as.data.frame(fit_reservations),aes(label=reservations))+xlim(-2,4)+ylim(-4,2)

lda of reservations

reservation<-factor(CMP_bbs_pcap_join_pcaponly_pcapsum$reservatio)
reservation_min3<-reservation[!(reservation %in% c("BK","EC","GP","HU","WA"))]

birdcomm_bin_min3<-birdcomm_bin[!(CMP_bbs_pcap_join_pcaponly_pcapsum$reservatio %in% c("BK","EC","GP","HU","WA")),]

birdcomm_bin_min3_drop1<-birdcomm_bin_min3[colSums(birdcomm_bin_min3) > 1]



color_resid_dropconstant<-color_resid[(colnames(birdcomm_bin) %in% colnames(birdcomm_bin_min3_drop1))]


lda_birdreserv<-lda(birdcomm_bin_min3_drop1, grouping = reservation_min3)
ggord(lda_birdreserv, reservation_min3, xlim=c(-15,15),ylim = c(-20, 20),txt=NULL,arrow=NULL)
ggord(lda_birdreserv, reservation_min3, xlim=c(-25,25),ylim = c(-20, 20),txt=NULL,arrow=NULL,alpha=0,alpha_el=0.5)
ggord(lda_birdreserv, reservation_min3, xlim=c(-25,25),ylim = c(-20, 20),alpha=0,alpha_el=0.5,veccol=color_resid_dropconstant,labcol=color_resid_dropconstant)

ggord(lda_birdreserv, reservation_min3, xlim=c(-25,25),ylim = c(-20, 20),veccol=color_resid_dropconstant,labcol=color_resid_dropconstant)


ggord(lda_birdreserv, reservation_min3, xlim=c(-10,10),ylim = c(-10, 10),alpha=0,alpha_el=0.5,veccol=color_resid_dropconstant,labcol=color_resid_dropconstant)

ggord(lda_birdreserv, reservation_min3, xlim=c(-7.5,7.5),ylim = c(-5, 6),alpha=0,alpha_el=0.5,var_sub = c("ACFL","HOWA","PIWO","SOSP"))


spe.class <- predict(lda_birdreserv)$class

# Posterior probabilities that the objects belong to those
# groups
spe.post <- predict(lda_birdreserv)$posterior

# Table of prior vs. predicted classifications
(spe.table <- table(reservation_min3, spe.class))


# Proportion of corrected classification
diag(prop.table(spe.table, 1))

Community associations

Now, we can also look at how bird communities are differentiated between community types.

community<-factor(CMP_bbs_pcap_join_pcaponly_pcapsum$community.x)

p_community<-rda(birdcomm_bin~community,CMP_bbs_pcap_join_pcaponly_pcapsum,scale=T)

community_fitbirds<-envfit(p_community,birdcomm_bin)

community_fit<-envfit(p_community~community,data=CMP_bbs_pcap_join_pcaponly_pcapsum,scale=T)


CMP_bbs_pcap_join_pcaponly_pcapsum$site<-rownames(CMP_bbs_pcap_join_pcaponly_pcapsum)

plot_df_community <- scores(p_community, display = "sites") %>% 
  as.data.frame() %>% 
  rownames_to_column("site") %>% 
  full_join(CMP_bbs_pcap_join_pcaponly_pcapsum, by = "site")

plot_rda_community <- ggplot(plot_df_community, aes(x = RDA1, y = RDA2, color = community)) +
  geom_point(size = 3, alpha = 0.8) +
  stat_ellipse(linetype = 2, size = 1) +
  labs(title = "RDA")
plot_rda_community

fitcommunity_pvals <- community_fitbirds$vectors$pvals %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  dplyr::rename("pvals" = ".")

# extract coordinates for species, only keep species with p-val = 0.001
fit_community_spp <- community_fitbirds %>% 
  scores(., display = "vectors") %>% 
  as.data.frame() %>% 
  rownames_to_column("species") %>% 
  full_join(., fitcommunity_pvals, by = "species") %>% 
  filter(pvals == 0.001)
fit_community_spp
##    species        RDA1         RDA2 pvals
## 1     ACFL -0.70195248  0.097941485 0.001
## 2     AMCR -0.26483267  0.156058987 0.001
## 3     BAOR  0.45535259 -0.100215702 0.001
## 4     BARS  0.41614862  0.128649059 0.001
## 5     BCCH -0.25914225  0.186621339 0.001
## 6     BEKI  0.07623645  0.304260844 0.001
## 7     CARW  0.19634245 -0.358991916 0.001
## 8     CEDW  0.50793156 -0.190529183 0.001
## 9     COGR  0.41281036  0.086914877 0.001
## 10    COYE  0.54462857  0.055690572 0.001
## 11    DEJU -0.37274656  0.195628876 0.001
## 12    EAKI  0.38558309  0.275585839 0.001
## 13    EAWP -0.54367957  0.191540154 0.001
## 14    EUST  0.61024663  0.132116554 0.001
## 15    GRCA  0.53815426 -0.159427712 0.001
## 16    HAWO -0.30118219  0.004202757 0.001
## 17    HOFI  0.29177592  0.044619987 0.001
## 18    HOWA -0.44401583  0.047422992 0.001
## 19    HOWR  0.28559364 -0.072630263 0.001
## 20    INBU  0.35169318 -0.145871019 0.001
## 21    KILL  0.25517824  0.354983330 0.001
## 22    MODO  0.51137295  0.027654563 0.001
## 23    NOFL  0.26754080  0.099347369 0.001
## 24    NRWS  0.32290594  0.402369183 0.001
## 25    OROR  0.66614724 -0.071544010 0.001
## 26    PIWO -0.19455428  0.313914955 0.001
## 27    PUFI  0.24916888  0.638570907 0.001
## 28    RBGR  0.31544337 -0.032567502 0.001
## 29    REVI -0.40938637  0.140627611 0.001
## 30    RWBL  0.62715213  0.018320407 0.001
## 31    SCTA -0.55217353  0.233164863 0.001
## 32    SOSP  0.60068008 -0.143602772 0.001
## 33    TRES  0.50591133  0.231005780 0.001
## 34    WAVI  0.63303103  0.006395845 0.001
## 35    WBNU -0.48857239 -0.043518576 0.001
## 36    WIFL  0.49797600  0.196922661 0.001
## 37    WOTH -0.31149124 -0.067476593 0.001
## 38    YEWA  0.72047250  0.049710859 0.001
fit_community <- community_fit %>% 
  scores(., display = "factors") %>% 
  as.data.frame() %>%
  rownames_to_column("community")

rda_communityn_plot_new <- ggplot(plot_df_community, aes(x = RDA1, y = RDA2)) +
  coord_fixed() +
  geom_point(aes(color = community), size = 3, alpha = 0.8) +
  geom_segment(data = fit_community_spp, aes(x = 0, xend = RDA1, y = 0, yend = RDA2),
               col = "black") +
  geom_text(data = fit_community_spp, aes(label = species))+
  geom_text(data=as.data.frame(fit_community),aes(label=community))
rda_communityn_plot_new

ggplot(plot_df_community, aes(x = RDA1, y = RDA2)) +
  coord_fixed() +
  geom_text(data=as.data.frame(fit_community),aes(label=community))+xlim(-2,4)+ylim(-1,5)

ggplot(plot_df_community, aes(x = RDA1, y = RDA2)) +
  coord_fixed() +
  geom_text(data=as.data.frame(fit_community_spp),aes(label=species))+xlim(-1,1)+ylim(-1,1)

For these ordinations, RDA1 seems to differentiate birds along an approximate gradient of forest cover - with negative loadings indicating more hardwood-associated bird communities and more positive loadings indicating more mesic/meadow-associated areas. Intriguingly, RDA2 then groups Mesic Meadows out from all other community types - with more positive values indicating more Mesic Meadow-associated birds.

Neotropical migrants: Acadian Fly-Catcher, Baltimore Oriole, Barn Swallow, Common Yellowthroat, Eastern Kingbird, Eastern Wood-Pewee, Hooded Warbler, Indigo Bunting, Orchard Oriole, Rose-Breasted Grosbeak, Red-Eyed Vireo, Scarlet Tanager, Warbling Vireo, Willow Flycatcher, Wood Thrush, Yellow Warbler = 16 species

Resident: Carolina Wren, European Starling, Hairy Woodpecker, House Sparrow, Pileated Woodpecker, Song Sparrow, White-Breasted Nuthatch = 7 species

Short-distance migrant: Brown Thrasher, Cedar Waxwing, Common Grackle, Gray Catbird, House Wren, Killdeer, Mourning Dove, Northern Rough-winged Swallow, Purple Finch, Red-winged Blackbird, Tree Swallow = 11 species

Resident or migratory: Dark-eyed Junco = 1 species

We also can explore linear discriminant analysis:

community<-factor(CMP_bbs_pcap_join_pcaponly_pcapsum$community.x)

birdcomm_bin_drop1<-birdcomm_bin[colSums(birdcomm_bin_min3) > 1]


color_resid_drop1<-color_resid[(colnames(birdcomm_bin) %in% colnames(birdcomm_bin_drop1))]


lda_birdcomm<-lda(birdcomm_bin_drop1, grouping = community)
lda_birdcomm_full<-lda(birdcomm_bin, grouping = community)

ggord(lda_birdcomm, community, xlim=c(-15,30),ylim = c(-15, 15),txt=NULL,arrow=NULL)
ggord(lda_birdcomm, community, xlim=c(-15,30),ylim = c(-15, 15),txt=NULL,arrow=NULL,alpha=0,alpha_el=0.5)
ggord(lda_birdcomm, community, xlim=c(-15,30),ylim = c(-15, 15),alpha=0,alpha_el=0.5,labcol=color_resid_drop1)

ggord(lda_birdcomm_full, community, xlim=c(-15,30),ylim = c(-15, 15),alpha=0,alpha_el=0.5,labcol=color_resid)

ggord(lda_birdcomm_full, community, xlim=c(-10,25),ylim = c(-7.5, 12.5),alpha=0,alpha_el=0.5,var_sub = c("ACFL","HOWA","PIWO","SOSP"))

lda

co-occurrence networks

We can also see which bird species co-occur together.

CMP_bbs_pcap_join_pcaponly_commsumm<-CMP_bbs_pcap_join_pcaponly %>% 
  group_by(community,species_4_) %>%
  summarise(n=n()) %>%
  spread(species_4_,n) %>%
  replace(is.na(.),0) 
CMP_bbs_pcap_join_pcaponly_commsumm<-column_to_rownames(CMP_bbs_pcap_join_pcaponly_commsumm,var = "community")

CMP_bbs_pcap_join_pcaponly_commsumm<-CMP_bbs_pcap_join_pcaponly_commsumm[,-1]

CMP_bbs_pcap_join_pcaponly_commsumm_presabs<-CMP_bbs_pcap_join_pcaponly_commsumm %>% mutate_if(is.numeric, ~1 * (. >= 1))

CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t<-t(CMP_bbs_pcap_join_pcaponly_commsumm_presabs)

CMP_bbs_pcap_join_pcaponly_reservsumm<-CMP_bbs_pcap_join_pcaponly %>% 
  group_by(reservatio,species_4_) %>%
  summarise(n=n()) %>%
  spread(species_4_,n) %>%
  replace(is.na(.),0) 
CMP_bbs_pcap_join_pcaponly_reservsumm<-column_to_rownames(CMP_bbs_pcap_join_pcaponly_reservsumm,var = "reservatio")

CMP_bbs_pcap_join_pcaponly_reservsumm<-CMP_bbs_pcap_join_pcaponly_reservsumm[,-1]

CMP_bbs_pcap_join_pcaponly_reservsumm_presabs<-CMP_bbs_pcap_join_pcaponly_reservsumm %>% mutate_if(is.numeric, ~1 * (. >= 1))

CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t<-t(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs)



birdcomm_bin_t<-t(birdcomm_bin)


BBSMigrants<-read.csv("G:/NaturalResources/Byer/datasets/BBS/BBS Migants.csv",header=T)

BBSMigrants_sub<-BBSMigrants[BBSMigrants$SpeciesCode %in% colnames(birdcomm_bin),]

BBSMigrants_sub_reorder<-BBSMigrants_sub[match(rownames(birdcomm_bin_t), BBSMigrants_sub$SpeciesCode),]

Residency<-BBSMigrants_sub_reorder$Residency

color_resid<-Residency

color_resid[color_resid %in% "NE"]<-"blue"

color_resid[color_resid %in% "M"]<-"green"

color_resid[color_resid %in% "R"]<-"red"


# presence/absence across plots
co <- print(cooccur(birdcomm_bin_t, spp_names = TRUE))

co[, "sp1_name"] == rownames(birdcomm_bin_t)[co$sp1]
co[, "sp2_name"] == rownames(birdcomm_bin_t)[co$sp2]



nodes <- data.frame(id = 1:nrow(birdcomm_bin_t),
                    label = rownames(birdcomm_bin_t),
                    color = color_resid,
                    shadow = TRUE) 
edges <- data.frame(from = co$sp1, to = co$sp2,
                    color = ifelse(co$p_lt <= 0.05, "#B0B2C1", "#3C3F51"),
                    dashes = ifelse(co$p_lt <= 0.05, TRUE, FALSE))

cooc<-cooccur(birdcomm_bin_t, spp_names = TRUE)

coccur

# presence/absence across reservations


co_reserv <- print(cooccur(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t, spp_names = TRUE))

co_reserv[, "sp1_name"] == rownames(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t)[co_reserv$sp1]
co_reserv[, "sp2_name"] == rownames(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t)[co_reserv$sp2]


nodes_reserv <- data.frame(id = 1:nrow(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t),
                    label = rownames(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t),
                    color = color_resid,
                    shadow = TRUE) 
edges_reserv <- data.frame(from = co_reserv$sp1, to = co_reserv$sp2,
                    color = ifelse(co_reserv$p_lt <= 0.05, "#B0B2C1", "#3C3F51"),
                    dashes = ifelse(co_reserv$p_lt <= 0.05, TRUE, FALSE))

coocc_reserv<-cooccur(CMP_bbs_pcap_join_pcaponly_reservsumm_presabs_t, spp_names = TRUE)



# presence/absence across habitats

co_comm <- print(cooccur(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t, spp_names = TRUE))

co_comm[, "sp1_name"] == rownames(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t)[co_comm$sp1]
co_comm[, "sp2_name"] == rownames(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t)[co_comm$sp2]


nodes_comm <- data.frame(id = 1:nrow(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t),
                    label = rownames(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t),
                    color = color_resid,
                    shadow = TRUE) 
edges_comm <- data.frame(from = co_comm$sp1, to = co_comm$sp2,
                    color = ifelse(co_comm$p_lt <= 0.05, "#B0B2C1", "#3C3F51"),
                    dashes = ifelse(co_comm$p_lt <= 0.05, TRUE, FALSE))

coocc_comm<-cooccur(CMP_bbs_pcap_join_pcaponly_commsumm_presabs_t, spp_names = TRUE)
visNetwork(nodes = nodes_comm, edges = edges_comm) %>%
    visIgraphLayout(layout = "layout_with_kk")
plot(coocc_comm)

plot(coocc_reserv)

Now pRDA - with variance partitioning.

As a final sanity check, it can sometimes be difficult to disentangle geographic effects from environmental effects in these sorts of analyses. For example, what if (hypothetically) cover of seedless vascular plants is negatively associated with geographic coordinates? Thus, we might want to briefly check if the variance explained by our environmental axes is (or is not) confounded with geography. To do so, we will use the varpart() function, which partitions variance between model components:

vegecomm_latlong<-CMP_bbs_pcap_join_pcaponly_pcapsum[,3:26]

pcap_geog<-varpart(birdcomm_bin,~ tol_rel + svp + dicot + cyper,~longitude+latitude,data=vegecomm_latlong)
plot(pcap_geog)

So - most of this variation is associated with these top covariates (X1), and NOT with latitude and longitude alone (X2). Good to see - this means we can be confident that these are actual environmental effects!

community richness metrics

Next, we can explore the relationships between species richness and plot characteristics. We will start with plot-level explorations.

plot-level analyses

plot-level richness and various indicators

Now, we will produce some exploratory models and plots of richness against basic indicators of vegetative quality, including the Floristic Quality Indicator (FQI) and the Vegetative Index of Biotic Integrity (VIBI).

## 
## Call:
## lm(formula = S ~ vibifq, data = vegecomm_richness)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -17.0236  -4.1863  -0.1937   4.0359  19.1247 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 28.32917    1.07290  26.404   <2e-16 ***
## vibifq      -0.04776    0.02100  -2.274   0.0243 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 6.203 on 162 degrees of freedom
## Multiple R-squared:  0.03093,    Adjusted R-squared:  0.02495 
## F-statistic:  5.17 on 1 and 162 DF,  p-value: 0.02429
## 
## Call:
## lm(formula = S ~ fqi, data = vegecomm_richness)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -17.1623  -4.4496  -0.0736   4.0143  19.5003 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 27.93473    1.44131  19.381   <2e-16 ***
## fqi         -0.09958    0.07574  -1.315     0.19    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 6.268 on 162 degrees of freedom
## Multiple R-squared:  0.01056,    Adjusted R-squared:  0.004449 
## F-statistic: 1.728 on 1 and 162 DF,  p-value: 0.1905

Somewhat unexpectedly, this seems to suggest that higher VIBI scores actually produce slightly less species-rich communities. What could be causing this? Well, to start - perhaps the number of surveys for each plot may be influencing this.

We can generate a summary of the number of surveys for each plot.

So the number of surveys clearly has an effect on the species richness of the site. This is somewhat difficult to account for, but we will attempt to do so using mixed effects models. I then use Akaike’s Information Criterion (AIC for short) to rank these models. The lowest number is the best, and any model within 2 AIC of the top model is potentially worth interpreting.

## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ vibifq + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4338.1
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.6272 -0.6938 -0.1159  0.6506  3.4401 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.751   2.398   
##  Residual              13.659   3.696   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 14.40949    0.52035  27.692
## vibifq      -0.02979    0.01011  -2.945
## 
## Correlation of Fixed Effects:
##        (Intr)
## vibifq -0.892
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ vibifqnotrees + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4344.3
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5644 -0.6912 -0.1017  0.6393  3.4613 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.144   2.479   
##  Residual              13.651   3.695   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##               Estimate Std. Error t value
## (Intercept)   13.60027    0.46329  29.356
## vibifqnotrees -0.01666    0.01195  -1.395
## 
## Correlation of Fixed Effects:
##             (Intr)
## vibifqnotrs -0.855
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ carex + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4341.1
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5143 -0.6878 -0.0932  0.6348  3.5104 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.247   2.499   
##  Residual              13.635   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 12.73705    0.40224   31.67
## carex        0.09470    0.09767    0.97
## 
## Correlation of Fixed Effects:
##       (Intr)
## carex -0.800
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ cyper + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4341
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5231 -0.6865 -0.0923  0.6361  3.5144 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.236   2.497   
##  Residual              13.635   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 12.70712    0.40043  31.734
## cyper        0.09970    0.09323   1.069
## 
## Correlation of Fixed Effects:
##       (Intr)
## cyper -0.798
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ dicot + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4338.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.4759 -0.7094 -0.0914  0.6311  3.5429 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.972   2.444   
##  Residual              13.617   3.690   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 11.77658    0.54658  21.546
## dicot        0.05340    0.02071   2.578
## 
## Correlation of Fixed Effects:
##       (Intr)
## dicot -0.900
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ shade + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4343.4
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.4759 -0.6917 -0.0955  0.6352  3.5320 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.22    2.494   
##  Residual              13.63    3.691   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 12.45647    0.49909  24.958
## shade        0.02703    0.01995   1.355
## 
## Correlation of Fixed Effects:
##       (Intr)
## shade -0.876
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ hydro + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4336.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.4494 -0.6753 -0.0787  0.6392  3.4727 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.878   2.425   
##  Residual              13.633   3.692   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 12.51440    0.30523  40.999
## hydro        0.09764    0.03556   2.746
## 
## Correlation of Fixed Effects:
##       (Intr)
## hydro -0.632
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ shrub + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4338.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5445 -0.6905 -0.0868  0.6392  3.4783 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.255   2.501   
##  Residual              13.641   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.1936     0.3126  42.208
## shrub        -0.3018     0.4145  -0.728
## 
## Correlation of Fixed Effects:
##       (Intr)
## shrub -0.635
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ svp + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4341.1
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5256 -0.6802 -0.1002  0.6338  3.4852 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.30    2.510   
##  Residual              13.63    3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 13.00541    0.31827  40.863
## svp          0.03293    0.15353   0.214
## 
## Correlation of Fixed Effects:
##     (Intr)
## svp -0.649
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ ap + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4335.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5304 -0.6816 -0.0968  0.6342  3.4941 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.285   2.507   
##  Residual              13.641   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.0838     0.3463  37.777
## ap           -0.3422     2.4707  -0.139
## 
## Correlation of Fixed Effects:
##    (Intr)
## ap -0.716
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ bryo + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4320.8
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5799 -0.6796 -0.0874  0.6408  3.5222 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.662   2.379   
##  Residual              13.629   3.692   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.6849     0.2993  45.720
## bryo        -42.5346    12.3590  -3.442
## 
## Correlation of Fixed Effects:
##      (Intr)
## bryo -0.625
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ sens_rel + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4324.5
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5796 -0.7120 -0.1165  0.6401  3.5406 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.501   2.345   
##  Residual              13.674   3.698   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.7822     0.3113  44.276
## sens_rel     -4.8617     1.3591  -3.577
## 
## Correlation of Fixed Effects:
##          (Intr)
## sens_rel -0.668
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ tol_rel + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4318.3
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.7018 -0.6931 -0.1086  0.6529  3.4039 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.191   2.278   
##  Residual              13.647   3.694   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  11.7966     0.3554  33.194
## tol_rel       3.8836     0.8575   4.529
## 
## Correlation of Fixed Effects:
##         (Intr)
## tol_rel -0.769
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ fqi + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4342.7
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5791 -0.6896 -0.1005  0.6455  3.4619 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.19    2.488   
##  Residual              13.65    3.694   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 13.81221    0.70470  19.600
## fqi         -0.04256    0.03690  -1.153
## 
## Correlation of Fixed Effects:
##     (Intr)
## fqi -0.940
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ inv + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4333.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5179 -0.6802 -0.0944  0.6357  3.5144 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.165   2.483   
##  Residual              13.647   3.694   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)   13.000      0.243  53.489
## inv            3.754      2.808   1.337
## 
## Correlation of Fixed Effects:
##     (Intr)
## inv -0.149
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ small_tree + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4335.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5411 -0.6780 -0.0925  0.6315  3.4833 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.292   2.508   
##  Residual              13.637   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.1468     0.4145  31.718
## small_tree   -0.6787     2.3502  -0.289
## 
## Correlation of Fixed Effects:
##            (Intr)
## small_tree -0.812
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ subcanopy + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4335.8
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5265 -0.6818 -0.0950  0.6331  3.4924 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.289   2.508   
##  Residual              13.639   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.0216     0.2914  44.691
## subcanopy     0.3731     2.1632   0.172
## 
## Correlation of Fixed Effects:
##           (Intr)
## subcanopy -0.557
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ canopy + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4327.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.7094 -0.6946 -0.1010  0.6303  3.6247 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  5.858   2.420   
##  Residual              13.637   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  14.7228     0.6473  22.745
## canopy       -8.1301     2.9181  -2.786
## 
## Correlation of Fixed Effects:
##        (Intr)
## canopy -0.931
## Linear mixed model fit by REML ['lmerMod']
## Formula: S_plotdate ~ 1 + (1 | simp_plot)
##    Data: vegecomm_bycount
## 
## REML criterion at convergence: 4339.2
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.5268 -0.6836 -0.0971  0.6333  3.4994 
## 
## Random effects:
##  Groups    Name        Variance Std.Dev.
##  simp_plot (Intercept)  6.227   2.495   
##  Residual              13.641   3.693   
## Number of obs: 763, groups:  simp_plot, 164
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  13.0488     0.2411   54.12
## 
## Model selection based on AICc:
## 
##       K    AICc Delta_AICc AICcWt Cum.Wt   Res.LL
## Mod16 4 4326.31       0.00   0.75   0.75 -2159.13
## Mod2  4 4328.88       2.57   0.21   0.96 -2160.41
## Mod10 4 4332.53       6.22   0.03   0.99 -2162.24
## Mod3  4 4335.67       9.36   0.01   1.00 -2163.81
## Mod9  4 4341.60      15.30   0.00   1.00 -2166.78
## Mod1  4 4343.63      17.32   0.00   1.00 -2167.79
## Mod13 4 4343.66      17.36   0.00   1.00 -2167.81
## Mod14 4 4343.88      17.58   0.00   1.00 -2167.92
## Mod8  4 4344.70      18.39   0.00   1.00 -2168.32
## Mod19 3 4345.27      18.96   0.00   1.00 -2169.62
## Mod17 4 4346.17      19.86   0.00   1.00 -2169.06
## Mod6  4 4346.62      20.31   0.00   1.00 -2169.28
## Mod12 4 4346.68      20.38   0.00   1.00 -2169.32
## Mod5  4 4349.06      22.75   0.00   1.00 -2170.50
## Mod15 4 4349.16      22.85   0.00   1.00 -2170.55
## Mod4  4 4349.17      22.86   0.00   1.00 -2170.56
## Mod7  4 4350.72      24.42   0.00   1.00 -2171.34
## Mod11 4 4351.45      25.14   0.00   1.00 -2171.70
## Mod18 4 4352.37      26.06   0.00   1.00 -2172.16

So richness - at a plot level, and after accounting for plot identity - is determined by how many tolerant species are in the associated plot. And this is much more predictive than any other model.

Here is the plot for this top model:

## `geom_smooth()` using formula 'y ~ x'

We can also verify that our mixed effects model fits better compared to the fixed effects model.

Rich_tol_rel_fixed<-lm(S_plotdate~tol_rel,vegecomm_bycount)
summary(Rich_tol_rel_fixed)
## 
## Call:
## lm(formula = S_plotdate ~ tol_rel, data = vegecomm_bycount)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -10.5052  -2.8223  -0.5578   2.7377  19.9775 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  11.6566     0.2402  48.522  < 2e-16 ***
## tol_rel       3.7289     0.5972   6.244 7.08e-10 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 4.291 on 761 degrees of freedom
## Multiple R-squared:  0.04874,    Adjusted R-squared:  0.04749 
## F-statistic: 38.99 on 1 and 761 DF,  p-value: 7.085e-10
anova(Rich_tol_rel, Rich_tol_rel_fixed) 
## refitting model(s) with ML (instead of REML)
## Data: vegecomm_bycount
## Models:
## Rich_tol_rel_fixed: S_plotdate ~ tol_rel
## Rich_tol_rel: S_plotdate ~ tol_rel + (1 | simp_plot)
##                    npar    AIC    BIC  logLik deviance  Chisq Df Pr(>Chisq)    
## Rich_tol_rel_fixed    3 4391.9 4405.8 -2193.0   4385.9                         
## Rich_tol_rel          4 4326.6 4345.2 -2159.3   4318.6 67.289  1  2.345e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

This confirms that we chose correctly - the mixed effects model fits better than the fixed effects-only model.

We can also inspect how this observation-level mixed effect model compares to a plot-level, fixed effect model (in other words - a view that just looks at richness at a plot level - aggregating over observations).

S_tol_rel<-lm(S~tol_rel,vegecomm_richness)
confint(S_tol_rel)
##                2.5 %    97.5 %
## (Intercept) 22.88094 25.853189
## tol_rel      1.96969  9.053297
confint(Rich_tol_rel)
## Computing profile confidence intervals ...
##                 2.5 %    97.5 %
## .sig01       1.845565  2.700243
## .sigma       3.493475  3.916023
## (Intercept) 11.100919 12.494418
## tol_rel      2.204396  5.564987

We can see that, while the covariate estimate for the plot-level model is higher, it is also estimated with much more variance (its confidence intervals are wider). This is not surprising - our functional sample size for this dataset is 164 plots. In contrast, while the observation-level mixed-effects model has a lower covariate estimate, we have tighter confidence intervals around this estimate - likely by virtue of a larger number of samples and a more effectively parameterized model.

reservation-level analyses

Now we are going to re-summarize this dataset at a reservation-level. While we will have limited power for many comparisons of interest, this could provide some indication of whether covariate relationships vary across scales.

This doesn’t quite get at what we want - this displays species accumulation across reservations after accounting for survey effort per reservation. Let’s try exploring reservation-by-reservation rarefaction with the previous observation-level dataset.

With the plot-level data, we could easily account for variation in survey effort across plots with a mixed model design, but this case is a bit more complicated. We are interested in reservation-level species richness, but know that reservations were visited different numbers of times - based on the number of plots and the number of surveys/plot. Thus, the easiest thing to start with is simply using species richness estimates interpolated to the least number of surveys per reservation (3, in our case).

Now we can proceed with exploring richness patterns across reservations.

## 
## Call:
## lm(formula = interrich_n3 ~ vibifq, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.9895 -1.8914  0.0771  2.0346  4.9142 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  19.2073     1.8849  10.190 7.39e-08 ***
## vibifq        0.1274     0.0474   2.688   0.0177 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.745 on 14 degrees of freedom
## Multiple R-squared:  0.3405, Adjusted R-squared:  0.2933 
## F-statistic: 7.227 on 1 and 14 DF,  p-value: 0.01766
## 
## Call:
## lm(formula = interrich_n3 ~ vibifqnotrees, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.3014 -1.3851 -0.2547  1.5610  4.8501 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   19.71868    1.40132   14.07 1.18e-09 ***
## vibifqnotrees  0.16621    0.04947    3.36  0.00467 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.515 on 14 degrees of freedom
## Multiple R-squared:  0.4464, Adjusted R-squared:  0.4069 
## F-statistic: 11.29 on 1 and 14 DF,  p-value: 0.00467
## 
## Call:
## lm(formula = interrich_n3 ~ carex, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.6119 -2.3320  0.1302  1.5981  6.0053 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  22.2520     1.6868  13.192 2.75e-09 ***
## carex         0.6247     0.5522   1.131    0.277    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.236 on 14 degrees of freedom
## Multiple R-squared:  0.08376,    Adjusted R-squared:  0.01832 
## F-statistic:  1.28 on 1 and 14 DF,  p-value: 0.2769
## 
## Call:
## lm(formula = interrich_n3 ~ cyper, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.9740 -2.4015  0.2932  1.6727  5.8817 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  22.5425     1.7090  13.190 2.75e-09 ***
## cyper         0.4864     0.5269   0.923    0.372    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.282 on 14 degrees of freedom
## Multiple R-squared:  0.05738,    Adjusted R-squared:  -0.009948 
## F-statistic: 0.8523 on 1 and 14 DF,  p-value: 0.3716
## 
## Call:
## lm(formula = interrich_n3 ~ dicot, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.9111 -1.8457  0.0889  1.9149  4.7618 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  20.6491     2.2152   9.321 2.21e-07 ***
## dicot         0.1592     0.1007   1.580    0.136    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.114 on 14 degrees of freedom
## Multiple R-squared:  0.1514, Adjusted R-squared:  0.09076 
## F-statistic: 2.497 on 1 and 14 DF,  p-value: 0.1364
## 
## Call:
## lm(formula = interrich_n3 ~ shade, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.5057 -1.7320 -0.0602  1.6767  5.0285 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 20.84811    1.89562  10.998 2.84e-08 ***
## shade        0.17383    0.09797   1.774   0.0978 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.054 on 14 degrees of freedom
## Multiple R-squared:  0.1836, Adjusted R-squared:  0.1253 
## F-statistic: 3.148 on 1 and 14 DF,  p-value: 0.09776
## 
## Call:
## lm(formula = interrich_n3 ~ hydro, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -3.2257 -1.9919 -0.0224  1.1333  5.2002 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  21.2706     1.1344  18.750 2.57e-11 ***
## hydro         0.6517     0.2249   2.897   0.0117 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.673 on 14 degrees of freedom
## Multiple R-squared:  0.3748, Adjusted R-squared:  0.3302 
## F-statistic: 8.394 on 1 and 14 DF,  p-value: 0.01171
## 
## Call:
## lm(formula = interrich_n3 ~ shrub, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.4970 -2.2197  0.3984  1.6878  4.6785 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   22.098      1.061  20.833 6.18e-12 ***
## shrub          6.064      2.594   2.338   0.0347 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.867 on 14 degrees of freedom
## Multiple R-squared:  0.2808, Adjusted R-squared:  0.2294 
## F-statistic: 5.466 on 1 and 14 DF,  p-value: 0.03475
## 
## Call:
## lm(formula = interrich_n3 ~ svp, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.8297 -2.2485 -0.0791  2.5216  5.7365 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  23.0925     1.0956  21.077 5.28e-12 ***
## svp           1.0359     0.9176   1.129    0.278    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.236 on 14 degrees of freedom
## Multiple R-squared:  0.08343,    Adjusted R-squared:  0.01797 
## F-statistic: 1.274 on 1 and 14 DF,  p-value: 0.2779
## 
## Call:
## lm(formula = interrich_n3 ~ ap, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.7087 -2.0774 -0.1786  1.6334  4.8219 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   21.706      1.547  14.034 1.22e-09 ***
## ap            23.910     14.428   1.657     0.12    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.091 on 14 degrees of freedom
## Multiple R-squared:  0.164,  Adjusted R-squared:  0.1043 
## F-statistic: 2.746 on 1 and 14 DF,  p-value: 0.1197
## 
## Call:
## lm(formula = interrich_n3 ~ bryo, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.6593 -1.8343 -0.1896  1.5095  5.2030 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   23.009      1.046   22.00 2.94e-12 ***
## bryo          59.804     44.312    1.35    0.199    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.18 on 14 degrees of freedom
## Multiple R-squared:  0.1151, Adjusted R-squared:  0.05192 
## F-statistic: 1.821 on 1 and 14 DF,  p-value: 0.1986
## 
## Call:
## lm(formula = interrich_n3 ~ sens_rel, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -3.9466 -2.1946 -0.3296  1.5746  5.9942 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   22.112      1.402  15.767 2.63e-10 ***
## sens_rel      13.128      8.433   1.557    0.142    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.121 on 14 degrees of freedom
## Multiple R-squared:  0.1476, Adjusted R-squared:  0.08667 
## F-statistic: 2.423 on 1 and 14 DF,  p-value: 0.1418
## 
## Call:
## lm(formula = interrich_n3 ~ tol_rel, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.8520 -1.9963  0.2494  1.3926  3.9695 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   28.181      1.624  17.350 7.32e-11 ***
## tol_rel      -10.591      3.684  -2.875   0.0122 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.68 on 14 degrees of freedom
## Multiple R-squared:  0.3713, Adjusted R-squared:  0.3264 
## F-statistic: 8.268 on 1 and 14 DF,  p-value: 0.01222
## 
## Call:
## lm(formula = interrich_n3 ~ fqi, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.0813 -1.4432 -0.3677  1.7574  5.0886 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  18.4035     2.4277    7.58 2.55e-06 ***
## fqi           0.3630     0.1525    2.38   0.0321 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.852 on 14 degrees of freedom
## Multiple R-squared:  0.288,  Adjusted R-squared:  0.2372 
## F-statistic: 5.664 on 1 and 14 DF,  p-value: 0.03208
## 
## Call:
## lm(formula = interrich_n3 ~ inv, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.3009 -2.1390  0.1538  1.7001  5.4281 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  23.6509     0.9491  24.920 5.36e-13 ***
## inv          30.0878    49.4189   0.609    0.552    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.337 on 14 degrees of freedom
## Multiple R-squared:  0.02579,    Adjusted R-squared:  -0.04379 
## F-statistic: 0.3707 on 1 and 14 DF,  p-value: 0.5524
## 
## Call:
## lm(formula = interrich_n3 ~ small_tree, data = vegecomm_reserv_richness)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -4.995 -2.762  0.536  1.819  4.382 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   22.208      1.992  11.147  2.4e-08 ***
## small_tree    13.070     13.815   0.946     0.36    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.277 on 14 degrees of freedom
## Multiple R-squared:  0.06009,    Adjusted R-squared:  -0.007046 
## F-statistic: 0.8951 on 1 and 14 DF,  p-value: 0.3602
## 
## Call:
## lm(formula = interrich_n3 ~ subcanopy, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -6.1982 -1.1147  0.3774  2.0300  3.7689 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   22.475      1.261  17.825 5.09e-11 ***
## subcanopy     25.264     17.153   1.473    0.163    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.145 on 14 degrees of freedom
## Multiple R-squared:  0.1342, Adjusted R-squared:  0.07232 
## F-statistic: 2.169 on 1 and 14 DF,  p-value: 0.1629
## 
## Call:
## lm(formula = interrich_n3 ~ canopy, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.3112 -2.6479  0.4868  1.8009  5.5576 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   27.441      4.374   6.273 2.05e-05 ***
## canopy       -17.408     21.275  -0.818    0.427    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.302 on 14 degrees of freedom
## Multiple R-squared:  0.04564,    Adjusted R-squared:  -0.02253 
## F-statistic: 0.6695 on 1 and 14 DF,  p-value: 0.4269
## 
## Call:
## lm(formula = interrich_n3 ~ 1, data = vegecomm_reserv_richness)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.5765 -2.3783  0.0258  2.0039  5.2136 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  23.9265     0.8164   29.31 1.17e-14 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.266 on 15 degrees of freedom
## 
## Model selection based on AICc:
## 
##       K  AICc Delta_AICc AICcWt Cum.Wt     LL
## Mod18 3 80.78       0.00   0.39   0.39 -36.39
## Mod8  3 82.73       1.95   0.15   0.54 -37.36
## Mod16 3 82.82       2.04   0.14   0.68 -37.41
## Mod17 3 83.59       2.80   0.10   0.77 -37.79
## Mod7  3 84.81       4.03   0.05   0.82 -38.40
## Mod12 3 84.97       4.19   0.05   0.87 -38.49
## Mod11 3 87.00       6.22   0.02   0.89 -39.50
## Mod19 2 87.17       6.38   0.02   0.91 -41.12
## Mod1  3 87.38       6.60   0.01   0.92 -39.69
## Mod6  3 87.62       6.84   0.01   0.93 -39.81
## Mod10 3 87.69       6.91   0.01   0.95 -39.85
## Mod14 3 87.94       7.16   0.01   0.96 -39.97
## Mod2  3 88.29       7.50   0.01   0.97 -40.14
## Mod4  3 88.85       8.06   0.01   0.97 -40.42
## Mod15 3 88.85       8.07   0.01   0.98 -40.43
## Mod13 3 89.25       8.47   0.01   0.99 -40.63
## Mod5  3 89.30       8.52   0.01   0.99 -40.65
## Mod3  3 89.50       8.71   0.00   1.00 -40.75
## Mod9  3 89.83       9.04   0.00   1.00 -40.91

although our power is a bit limited above, it does appear that the Vegetative Index of Biotic Integrity - at a reservation-level - does appear to predict bird species richness (as long as we do not include woody plants in that list!)

we can also plot out richness for each site:

In confirmation of our prior ordination plots, it now appears that Rocky River is one of the most species rich areas - followed by Hinckley, South Chagrin, Bedford, and Brecksville.

reservation shape features and species richness

While these vegetative associations are certainly important, it is often helpful to also think about how the shape of our reservations influences the species found within them. There is a rich body of literature on the effects of landscape context and configuration on ecological processes and patterns - and this is an area I am particularly interested in!

## 
## Call:
## lm(formula = interrich_n3 ~ acres, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -3.5631 -2.4973 -0.4665  2.3662  3.6307 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 2.183e+01  9.964e-01  21.907 3.12e-12 ***
## acres       1.427e-03  5.003e-04   2.853   0.0128 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.688 on 14 degrees of freedom
## Multiple R-squared:  0.3676, Adjusted R-squared:  0.3224 
## F-statistic: 8.137 on 1 and 14 DF,  p-value: 0.01278
## 
## Call:
## lm(formula = interrich_n3 ~ ai, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.0724 -1.9479  0.3464  2.3852  4.6071 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)
## (Intercept)   3.8654    14.9201   0.259    0.799
## ai            0.2148     0.1595   1.346    0.200
## 
## Residual standard error: 3.181 on 14 degrees of freedom
## Multiple R-squared:  0.1147, Adjusted R-squared:  0.05141 
## F-statistic: 1.813 on 1 and 14 DF,  p-value: 0.1995
## 
## Call:
## lm(formula = interrich_n3 ~ area_mn, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.0836 -1.8857  0.0032  2.5293  4.6198 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 2.238e+01  8.992e-01  24.893 5.44e-13 ***
## area_mn     1.334e-03  5.003e-04   2.667   0.0184 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.753 on 14 degrees of freedom
## Multiple R-squared:  0.3369, Adjusted R-squared:  0.2895 
## F-statistic: 7.112 on 1 and 14 DF,  p-value: 0.01841
## 
## Call:
## lm(formula = interrich_n3 ~ ca, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -3.5674 -2.4976 -0.4706  2.3698  3.6266 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 2.183e+01  9.961e-01  21.916  3.1e-12 ***
## ca          3.272e-04  1.148e-04   2.851   0.0128 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.689 on 14 degrees of freedom
## Multiple R-squared:  0.3673, Adjusted R-squared:  0.3222 
## F-statistic: 8.129 on 1 and 14 DF,  p-value: 0.01282
## 
## Call:
## lm(formula = interrich_n3 ~ cai_mn, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.8380 -1.1997 -0.0736  1.4644  5.0782 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 21.87439    1.68642  12.971 3.42e-09 ***
## cai_mn       0.05196    0.03769   1.379     0.19    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.172 on 14 degrees of freedom
## Multiple R-squared:  0.1196, Adjusted R-squared:  0.05667 
## F-statistic: 1.901 on 1 and 14 DF,  p-value: 0.1896
## 
## Call:
## lm(formula = interrich_n3 ~ circle_mn, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.1446 -1.3189 -0.2862  2.4754  4.5336 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)  
## (Intercept)   13.522      5.116   2.643   0.0193 *
## circle_mn     15.941      7.756   2.055   0.0590 .
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.963 on 14 degrees of freedom
## Multiple R-squared:  0.2318, Adjusted R-squared:  0.1769 
## F-statistic: 4.224 on 1 and 14 DF,  p-value: 0.05901
## 
## Call:
## lm(formula = interrich_n3 ~ clumpy, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.4175 -1.2864  0.0603  1.5948  3.6887 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)   
## (Intercept)   131.77      32.30   4.079  0.00113 **
## clumpy       -105.14      31.49  -3.339  0.00487 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.522 on 14 degrees of freedom
## Multiple R-squared:  0.4433, Adjusted R-squared:  0.4036 
## F-statistic: 11.15 on 1 and 14 DF,  p-value: 0.004868
## 
## Call:
## lm(formula = interrich_n3 ~ cohesion, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.6505 -1.6378  0.1534  2.0821  3.3417 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)  
## (Intercept) -64.3502    30.6532  -2.099   0.0544 .
## cohesion      0.9074     0.3150   2.881   0.0121 *
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.679 on 14 degrees of freedom
## Multiple R-squared:  0.3721, Adjusted R-squared:  0.3273 
## F-statistic: 8.298 on 1 and 14 DF,  p-value: 0.0121
## 
## Call:
## lm(formula = interrich_n3 ~ contig_mn, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.6781 -1.4373  0.0113  1.7757  5.5978 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   20.328      2.349   8.653 5.43e-07 ***
## contig_mn      5.937      3.659   1.623    0.127    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.101 on 14 degrees of freedom
## Multiple R-squared:  0.1583, Adjusted R-squared:  0.09815 
## F-statistic: 2.633 on 1 and 14 DF,  p-value: 0.127
## 
## Call:
## lm(formula = interrich_n3 ~ core_mn, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.1220 -1.9201  0.0065  2.4113  4.6225 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 2.244e+01  8.842e-01  25.379 4.17e-13 ***
## core_mn     1.513e-03  5.663e-04   2.672   0.0182 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.751 on 14 degrees of freedom
## Multiple R-squared:  0.3377, Adjusted R-squared:  0.2904 
## F-statistic: 7.139 on 1 and 14 DF,  p-value: 0.01823
## 
## Call:
## lm(formula = interrich_n3 ~ cpland, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -3.6712 -2.5859 -0.4077  2.2932  3.6402 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  21.9702     0.9793  22.434 2.25e-12 ***
## cpland        0.3844     0.1387   2.772    0.015 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.716 on 14 degrees of freedom
## Multiple R-squared:  0.3544, Adjusted R-squared:  0.3083 
## F-statistic: 7.685 on 1 and 14 DF,  p-value: 0.01498
## 
## Call:
## lm(formula = interrich_n3 ~ dcad, data = vegecomm_reserv_richness_struct)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.3593 -2.7674 -0.1255  1.5015  5.6289 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   22.595      1.206  18.739 2.59e-11 ***
## dcad         121.688     83.440   1.458    0.167    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.15 on 14 degrees of freedom
## Multiple R-squared:  0.1319, Adjusted R-squared:  0.06988 
## F-statistic: 2.127 on 1 and 14 DF,  p-value: 0.1668

multi-species occupancy modelling

MSOM - running different models

basic null model

bbs_occobject_null.occ.formula <- ~1
bbs_occobject_null.det.formula <- ~ 1
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.null <- msPGOcc(occ.formula = bbs_occobject_null.occ.formula, 
                  det.formula = bbs_occobject_null.det.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.null)
ppc.ms.null.out <- ppcOcc(out.ms.null, 'chi-squared', group = 1)
summary(ppc.ms.null.out)

waicOcc(out.ms.null)

building up complexity of detection model

bbs_occobject_null.occ.formula <- ~1
bbs_occobject_day.det.formula <- ~ scale(day)
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.detect.day <- msPGOcc(occ.formula = bbs_occobject_null.occ.formula, 
                  det.formula = bbs_occobject_day.det.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.detect.day)
ppc.ms.detect.day.out <- ppcOcc(out.ms.detect.day, 'chi-squared', group = 1)
summary(out.ms.detect.day)

waicOcc(out.ms.detect.day)

day and time-of-day

bbs_occobject_null.occ.formula <- ~1
bbs_occobject_daytod.det.formula <- ~ scale(day)+scale(tod)
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.detect.daytod <- msPGOcc(occ.formula = bbs_occobject_null.occ.formula, 
                  det.formula = bbs_occobject_daytod.det.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.detect.daytod)
ppc.ms.detect.day.out <- ppcOcc(out.ms.detect.daytod, 'chi-squared', group = 1)
summary(out.ms.detect.daytod)

waicOcc(out.ms.detect.daytod)

day, tod, quadratic day

bbs_occobject_null.occ.formula <- ~1
bbs_occobject_daytodquad.det.formula <- ~ scale(day)+scale(tod) +I(scale(day)^2)
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.detect.daytodquad<- msPGOcc(occ.formula = bbs_occobject_null.occ.formula, 
                  det.formula = bbs_occobject_daytodquad.det.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.detect.daytodquad)
ppc.ms.detect.day.out <- ppcOcc(out.ms.detect.daytodquad, 'chi-squared', group = 1)
summary(out.ms.detect.daytodquad)

waicOcc(out.ms.detect.daytodquad)

The best-supported model is within 2 WAIC of a simpler detection model - one that just includes day. So we will proceed with just using a linear term for day in our detectability submodels.

Now we will run several different occupancy submodels, once again evaluating fit for progressively more complicated models.

occupancy model with vibi-fq

bbs_occobject_vibifq.occ.formula <- ~ scale(vibifq)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.vibifq <- msPGOcc(occ.formula = bbs_occobject_vibifq.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.vibifq)
ppc.ms.vibifq.out <- ppcOcc(out.ms.vibifq, 'chi-squared', group = 1)
summary(ppc.ms.vibifq.out)


out.ms.bestdec.small <- msPGOcc(occ.formula = ~1, 
                       det.formula = bbs_occobject.det.best.formula, 
                       data = bbs_occobject, 
                       inits = ms.inits, 
                       n.samples = 30000, 
                       priors = ms.priors, 
                       n.omp.threads = 1, 
                       verbose = TRUE, 
                       n.report = 6000, 
                       n.burn = 10000,
                       n.thin = 50, 
                       n.chains = 3)


waicOcc(out.ms.bestdec.small)
waicOcc(out.ms.vibifq)

occupancy model with vibi-fq-notrees

bbs_occobject_vibifqnotrees.occ.formula <- ~ scale(vibifqnotrees)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.vibifqnotrees <- msPGOcc(occ.formula = bbs_occobject_vibifqnotrees.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.vibifqnotrees)
ppc.ms.vibifqnotrees.out <- ppcOcc(out.ms.vibifqnotrees, 'chi-squared', group = 1)
summary(ppc.ms.vibifqnotrees.out)

waicOcc(out.ms.vibifqnotrees)

occupancy model with all rda-supported covariates

bbs_occobject_fullrda.occ.formula <- ~ scale(tol_rel) + scale(svp) + scale(dicot) + scale(cyper) + scale(small_tree)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.fullrda <- msPGOcc(occ.formula = bbs_occobject_fullrda.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.fullrda)
ppc.ms.fullrda.out <- ppcOcc(out.ms.fullrda, 'chi-squared', group = 1)
summary(ppc.ms.fullrda.out)

waicOcc(out.ms.fullrda)

occupancy model with just tolerance/sensitivity

bbs_occobject_tolerance.occ.formula <- ~ scale(tol_rel)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.tolerance<- msPGOcc(occ.formula = bbs_occobject_tolerance.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.tolerance)
ppc.ms.tolerance.out <- ppcOcc(out.ms.tolerance, 'chi-squared', group = 1)
summary(ppc.ms.tolerance.out)

waicOcc(out.ms.tolerance)

global model

bbs_occobject_global.occ.formula <- ~ scale(tol_rel) + scale(svp) + scale(dicot) + scale(cyper) + scale(small_tree)+scale(shrub)+scale(hydro)+scale(subcanopy)+scale(canopy)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.global <- msPGOcc(occ.formula = bbs_occobject_global.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.global)
ppc.ms.global.out <- ppcOcc(out.ms.global, 'chi-squared', group = 1)
summary(ppc.ms.global.out)

waicOcc(out.ms.global)

global model - all non-correlated covariates (after removing some redundancy)

bbs_occobject_global.occ.formula <- ~ scale(tol_rel) + scale(svp) + scale(dicot) + scale(cyper) + scale(small_tree)+scale(shrub)+scale(hydro)+scale(subcanopy)+scale(canopy)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.global <- msPGOcc(occ.formula = bbs_occobject_global.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.global)
ppc.ms.global.out <- ppcOcc(out.ms.global, 'chi-squared', group = 1)
summary(ppc.ms.global.out)

waicOcc(out.ms.global)

just FQAI

bbs_occobject_fqi.occ.formula <- ~ scale(fqi)
bbs_occobject.det.best.formula <- ~ scale(day) 
N <- dim(bbs_occobject$y)[1]
ms.inits <- list(alpha.comm = 0, 
                 beta.comm = 0, 
                 beta = 0, 
                 alpha = 0,
                 tau.sq.beta = 1, 
                 tau.sq.alpha = 1, 
                 z = apply(bbs_occobject$y, c(1, 2), max, na.rm = TRUE))
ms.priors <- list(beta.comm.normal = list(mean = 0, var = 2.72),
                  alpha.comm.normal = list(mean = 0, var = 2.72), 
                  tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
                  tau.sq.alpha.ig = list(a = 0.1, b = 0.1))
out.ms.fqi <- msPGOcc(occ.formula = bbs_occobject_fqi.occ.formula, 
                  det.formula = bbs_occobject.det.best.formula, 
                  data = bbs_occobject, 
                  inits = ms.inits, 
                  n.samples = 30000, 
                  priors = ms.priors, 
                  n.omp.threads = 1, 
                  verbose = TRUE, 
                  n.report = 6000, 
                  n.burn = 10000,
                  n.thin = 50, 
                  n.chains = 3)


summary(out.ms.fqi)
ppc.ms.fqi.out <- ppcOcc(out.ms.fqi, 'chi-squared', group = 1)
summary(ppc.ms.fqi.out)

waicOcc(out.ms.fqi)

model selection

we can also print out a table of Widely Applicable Information Criterion (wAIC) values. The lower this is, the better the model fit.

AICc_table<-tibble(.rows = 10)

AICc_table$model<-c("Null","p ~ day", "p ~ day + time-of-day", "p ~ day^2 + day +tod", "p ~ day, psi ~ vibi-fq", "p ~ day, psi ~ vibi-fq-notree","p ~ day, psi ~ tolerant + seedless vascular + dicots + cyperaceae + small trees","p~day,psi~tolerant","p~day,psi~tolerant + seedless vascular + dicot + cyperaceae + small trees +shrubs+hydro+subcanopy+canopy","p~day,psi~fqi")

AICc_table$wAIC<-c(waicOcc(out.ms.null)[[3]],waicOcc(out.ms.detect.day)[[3]],waicOcc(out.ms.detect.daytod)[[3]],
                   waicOcc(out.ms.detect.daytodquad)[[3]],waicOcc(out.ms.vibifq)[[3]],waicOcc(out.ms.vibifqnotrees)[[3]],
                   waicOcc(out.ms.fullrda)[[3]],waicOcc(out.ms.tolerance)[[3]],waicOcc(out.ms.global)[[3]],waicOcc(out.ms.fqi)[[3]])
##   X                                                                                                    model     wAIC
## 9 9 p~day,psi~tolerant + seedless vascular + dicot + cyperaceae + small trees +shrubs+hydro+subcanopy+canopy 23165.73
## 7 7                          p ~ day, psi ~ tolerant + seedless vascular + dicots + cyperaceae + small trees 23185.00
## 5 5                                                                                   p ~ day, psi ~ vibi-fq 23190.57
## 8 8                                                                                       p~day,psi~tolerant 23323.25
## 6 6                                                                            p ~ day, psi ~ vibi-fq-notree 23372.44
## 4 4                                                                                     p ~ day^2 + day +tod 23755.71
## 2 2                                                                                                  p ~ day 23756.93
## 3 3                                                                                    p ~ day + time-of-day 23769.78
## 1 1                                                                                                     Null 23840.32

So, the top model is the global, followed by the stepwise-selected rda model.

Now, we plot based on this top model.

plotting using an RShiny app

While the below RShiny app should be fairly easy to use within the current webpage, you may also access this via: https://testudinidude.shinyapps.io/bbsapp/.

covariate plotting

Finally, we can also run some plots depicting covariate effects for each species. These should make it clear if and when species appear to be particularly related to certain vegetative characteristics - and thus may serve as “indicators” for these characteristics.

##        Process                       Species  Covariate    Mean     SD  X2.5CI   X50CI X97.5CI   Rhat  ESS  X5.0CI X95.0CI
## 1    Occupancy            Acadian Flycatcher  Intercept  0.2340 0.2189 -0.1936  0.2263  0.6652 1.0000 1200 -0.1116  0.5983
## 2    Occupancy              Alder Flycatcher  Intercept -4.6154 1.2222 -7.0511 -4.6699 -2.1794 1.0076  794 -6.5500 -2.5809
## 3    Occupancy                 American Crow  Intercept -0.0006 0.3910 -0.6121 -0.0505  0.9042 1.0243 1200 -0.5431  0.6397
## 4    Occupancy            American Goldfinch  Intercept  2.6936 0.8529  1.6175  2.5289  4.8081 1.0026  862  1.7358  4.2499
## 5    Occupancy              American Kestrel  Intercept -4.4353 1.3088 -6.8580 -4.4972 -1.9547 1.0133  557 -6.4682 -2.4585
## 6    Occupancy             American Redstart  Intercept -2.4841 0.5525 -3.4860 -2.5436 -1.3104 1.0089 1200 -3.3129 -1.5385
## 7    Occupancy                American Robin  Intercept  2.4787 0.3953  1.8250  2.4325  3.3823 1.0028 1060  1.9102  3.1850
## 8    Occupancy             American Woodcock  Intercept -4.1978 0.9036 -5.9506 -4.1849 -2.3962 1.0038  941 -5.6645 -2.7753
## 9    Occupancy                    Barred Owl  Intercept -3.2363 1.2162 -5.3244 -3.3502 -0.3969 1.0342  521 -4.9742 -1.2083
## 10   Occupancy                    Bald Eagle  Intercept -3.6512 1.1352 -5.6987 -3.7054 -1.2386 1.0080  617 -5.4050 -1.7567
## 11   Occupancy                  Bank Swallow  Intercept -4.2125 1.2134 -6.4725 -4.2291 -1.6513 1.0031  777 -6.0845 -2.2049
## 12   Occupancy              Baltimore Oriole  Intercept -0.1700 0.3474 -0.7735 -0.1887  0.6107 1.0052 1200 -0.6892  0.4565
## 13   Occupancy                  Barn Swallow  Intercept -1.8638 0.7451 -3.0358 -1.9710 -0.2046 1.0006  784 -2.8706 -0.4977
## 14   Occupancy        Black-capped Chickadee  Intercept  3.1328 0.8145  1.9918  2.9961  5.1309 1.0032  904  2.1168  4.6881
## 15   Occupancy             Belted Kingfisher  Intercept -0.9584 0.8347 -2.2092 -1.0724  0.9935 1.0167  692 -2.0568  0.4083
## 16   Occupancy         Blue-gray Gnatcatcher  Intercept  1.3498 0.4611  0.6351  1.2916  2.3720 1.0241 1200  0.7229  2.1047
## 17   Occupancy          Brown-headed Cowbird  Intercept  2.0201 0.4701  1.2236  1.9563  3.0685 1.0064 1200  1.3545  2.8841
## 18   Occupancy             Blue-headed Vireo  Intercept -4.2735 1.2975 -6.8127 -4.3253 -1.5128 1.0136  627 -6.3524 -2.0728
## 19   Occupancy                      Blue Jay  Intercept  2.2398 0.3895  1.6337  2.1909  3.1552 1.0017 1200  1.6981  2.9143
## 20   Occupancy                      Bobolink  Intercept -5.7820 1.6136 -9.0744 -5.6978 -2.6350 1.0039  711 -8.4656 -3.2912
## 21   Occupancy                 Brown Creeper  Intercept -2.2527 0.5140 -3.1811 -2.2674 -1.0675 1.0230  848 -3.0437 -1.3583
## 22   Occupancy                Brown Thrasher  Intercept -3.4277 0.9623 -5.2997 -3.4529 -1.5567 1.0059  925 -4.8878 -1.9107
## 23   Occupancy  Black-throated Green Warbler  Intercept -5.7915 1.6251 -9.2141 -5.6925 -2.9118 1.0302  629 -8.6299 -3.3163
## 24   Occupancy             Broad-winged Hawk  Intercept -3.7298 1.1294 -5.8219 -3.7773 -1.1904 1.0036  477 -5.4787 -1.7686
## 25   Occupancy           Blue-winged Warbler  Intercept -2.9899 0.7912 -4.3474 -3.0606 -1.2803 1.0175  637 -4.1170 -1.5804
## 26   Occupancy                  Canada Goose  Intercept -0.7118 1.3703 -2.6242 -0.9781  2.8594 1.0479  328 -2.3321  1.9595
## 27   Occupancy                 Carolina Wren  Intercept  0.1433 0.4059 -0.5532  0.1170  1.0327 1.0172 1134 -0.4608  0.8786
## 28   Occupancy                 Cedar Waxwing  Intercept -0.1525 0.3303 -0.7738 -0.1668  0.5337 1.0094 1200 -0.6659  0.3959
## 29   Occupancy              Cerulean Warbler  Intercept -5.8379 1.5697 -9.3620 -5.7413 -3.0339 1.0210  683 -8.5459 -3.3934
## 30   Occupancy              Chipping Sparrow  Intercept -0.7889 0.4604 -1.4935 -0.8463  0.3563 1.0065 1200 -1.4116  0.0532
## 31   Occupancy                 Chimney Swift  Intercept  1.1735 0.7033  0.2084  1.0528  2.9209 1.0057  743  0.3159  2.5192
## 32   Occupancy                 Cliff Swallow  Intercept -4.3270 1.3238 -6.9050 -4.3184 -1.6162 1.0091  534 -6.4709 -2.2634
## 33   Occupancy                Common Grackle  Intercept  0.3782 0.4638 -0.4308  0.3539  1.3987 1.0059 1424 -0.3112  1.1882
## 34   Occupancy                 Cooper's Hawk  Intercept -2.3554 0.6747 -3.4389 -2.4410 -0.6215 1.0091 1084 -3.2967 -1.0931
## 35   Occupancy           Common Yellowthroat  Intercept -1.1664 0.2481 -1.6332 -1.1675 -0.6921 1.0096 1200 -1.5555 -0.7677
## 36   Occupancy               Dark-eyed Junco  Intercept -2.0001 0.4388 -2.8216 -2.0218 -1.0838 1.0020 1309 -2.6929 -1.2480
## 37   Occupancy              Downy Woodpecker  Intercept  2.4885 0.7364  1.5419  2.3499  4.2868 1.0254  927  1.6396  3.6745
## 38   Occupancy              Eastern Bluebird  Intercept -0.6301 0.6177 -1.5838 -0.6968  0.7618 1.0236  959 -1.4835  0.5063
## 39   Occupancy              Eastern Kingbird  Intercept -3.2708 0.5131 -4.3102 -3.2560 -2.3405 1.0075 1200 -4.1229 -2.4817
## 40   Occupancy            Eastern Meadowlark  Intercept -4.2675 0.9014 -6.0429 -4.2885 -2.5616 1.0125 1018 -5.7338 -2.8291
## 41   Occupancy                Eastern Phoebe  Intercept -1.3365 0.4940 -2.1418 -1.3823 -0.2197 0.9996 1200 -2.0579 -0.4501
## 42   Occupancy                Eastern Towhee  Intercept -1.3633 0.3171 -1.9795 -1.3733 -0.7191 1.0053 1392 -1.8711 -0.8325
## 43   Occupancy            Eastern Wood-Pewee  Intercept  2.6790 0.4316  1.9619  2.6278  3.6219 1.0023 1200  2.0306  3.4415
## 44   Occupancy             European Starling  Intercept -2.0715 0.3652 -2.7766 -2.0797 -1.3748 1.0139 1403 -2.6555 -1.4657
## 45   Occupancy                 Field Sparrow  Intercept -3.2115 0.4084 -4.0221 -3.2029 -2.4672 1.0153 1200 -3.8895 -2.5739
## 46   Occupancy              Great Blue Heron  Intercept -1.9644 0.9871 -3.4305 -2.0844  0.5928 1.0164  466 -3.2598 -0.1648
## 47   Occupancy      Great Crested Flycatcher  Intercept  2.1668 1.1977  0.7160  1.8397  5.3658 1.0393  446  0.8515  4.6424
## 48   Occupancy              Great Horned Owl  Intercept -4.2320 1.4847 -6.9028 -4.3288 -0.8751 1.0422  375 -6.4214 -1.7492
## 49   Occupancy                  Gray Catbird  Intercept  0.0940 0.2271 -0.3244  0.0865  0.5830 1.0058 1200 -0.2695  0.4733
## 50   Occupancy                   Green Heron  Intercept -4.3484 1.3112 -6.8034 -4.4094 -1.4477 1.0012  655 -6.4703 -2.1233
## 51   Occupancy              Hairy Woodpecker  Intercept  1.0511 0.9566 -0.1954  0.8555  3.4640 1.0286  516 -0.0880  2.9360
## 52   Occupancy                  Herring Gull  Intercept -5.0533 1.0386 -7.2435 -5.0236 -3.2127 1.0140 1069 -6.8029 -3.4610
## 53   Occupancy                 Hermit Thrush  Intercept -4.7893 0.7420 -6.4398 -4.7193 -3.4954 1.0011 1084 -6.1808 -3.7270
## 54   Occupancy                   House Finch  Intercept -0.4395 0.8902 -1.6495 -0.6052  1.8106 1.0204  628 -1.5024  1.1533
## 55   Occupancy                 House Sparrow  Intercept -1.7705 0.3165 -2.3783 -1.7736 -1.1674 1.0046 1311 -2.2942 -1.2666
## 56   Occupancy                Hooded Warbler  Intercept -0.8936 0.2216 -1.3101 -0.8984 -0.4576 1.0076 1200 -1.2469 -0.5273
## 57   Occupancy                    House Wren  Intercept -0.1521 0.1789 -0.4930 -0.1495  0.1892 1.0116 1200 -0.4426  0.1477
## 58   Occupancy                Indigo Bunting  Intercept -0.1185 0.2077 -0.5105 -0.1196  0.3230 1.0047 1318 -0.4458  0.2416
## 59   Occupancy                      Killdeer  Intercept -2.9777 0.6070 -4.1287 -2.9659 -1.7107 1.0116 1200 -3.9554 -1.9875
## 60   Occupancy         Louisiana Waterthrush  Intercept -2.3514 0.5046 -3.2456 -2.3921 -1.2431 1.0108 1200 -3.1113 -1.4645
## 61   Occupancy                       Mallard  Intercept -2.2053 1.1945 -3.8810 -2.4349  0.9046 1.0732  327 -3.6680  0.1575
## 62   Occupancy                 Mourning Dove  Intercept -1.1253 0.5098 -2.0139 -1.1690 -0.0237 1.0128 1336 -1.8906 -0.2259
## 63   Occupancy             Northern Cardinal  Intercept  2.6612 0.4154  1.9569  2.6112  3.5935 1.0042 1301  2.0644  3.4162
## 64   Occupancy              Northern Flicker  Intercept  1.1312 1.1987 -0.4418  0.8662  4.4485 1.0076  489 -0.3055  3.4692
## 65   Occupancy               Northern Parula  Intercept -4.3980 1.1616 -6.6943 -4.4150 -1.9764 1.0175  907 -6.2715 -2.3755
## 66   Occupancy Northern Rough-winged Swallow  Intercept -2.0908 0.7159 -3.3175 -2.1448 -0.4619 1.0146 1083 -3.1526 -0.7288
## 67   Occupancy                Orchard Oriole  Intercept -2.5441 0.5165 -3.5647 -2.5497 -1.5591 1.0069 1200 -3.4127 -1.7076
## 68   Occupancy                      Ovenbird  Intercept -2.7411 0.3799 -3.4950 -2.7534 -1.9963 1.0017 1064 -3.3822 -2.0969
## 69   Occupancy           Pileated Woodpecker  Intercept  1.3278 1.2478 -0.2932  1.0140  4.5003 1.0028  486 -0.0992  3.8978
## 70   Occupancy                  Purple Finch  Intercept -4.6182 1.2931 -7.0651 -4.6342 -1.9387 1.0184  720 -6.7146 -2.5202
## 71   Occupancy                 Purple Martin  Intercept -5.7645 1.6389 -9.2771 -5.6859 -2.7333 1.0081  602 -8.6066 -3.3179
## 72   Occupancy        Rose-breasted Grosbeak  Intercept -0.0306 0.6400 -0.9290 -0.1319  1.4403 1.0027  873 -0.8291  1.0408
## 73   Occupancy              Ring-billed Gull  Intercept -2.5974 0.6158 -3.5624 -2.6476 -1.3133 1.0347  455 -3.4718 -1.6445
## 74   Occupancy         Red-breasted Nuthatch  Intercept -4.3215 1.3994 -6.8785 -4.3605 -1.1349 1.0129  532 -6.4637 -1.8609
## 75   Occupancy        Red-bellied Woodpecker  Intercept  3.1006 0.6479  2.0785  3.0266  4.5694 1.0042 1200  2.2019  4.2586
## 76   Occupancy                Red-eyed Vireo  Intercept  2.8748 0.4073  2.1383  2.8528  3.7559 1.0032 1787  2.2430  3.5901
## 77   Occupancy         Red-headed Woodpecker  Intercept -2.6122 0.9408 -4.1141 -2.7150 -0.5804 1.0135  471 -3.8820 -0.8964
## 78   Occupancy                   Rock Pigeon  Intercept -3.6747 1.0935 -5.7871 -3.7102 -1.4484 1.0108  660 -5.4487 -1.8426
## 79   Occupancy           Red-shouldered Hawk  Intercept  0.0300 1.3537 -2.1209 -0.1729  3.1940 1.0002  345 -1.7924  2.3426
## 80   Occupancy               Red-tailed Hawk  Intercept -0.6877 1.2705 -2.5205 -0.9232  2.6374 1.0338  302 -2.2580  1.7696
## 81   Occupancy     Ruby-throated Hummingbird  Intercept  2.0525 1.3900  0.0207  1.8108  5.4609 1.0240  537  0.2036  4.7782
## 82   Occupancy          Red-winged Blackbird  Intercept -0.9361 0.2133 -1.3488 -0.9352 -0.5358 1.0001 1200 -1.2832 -0.5863
## 83   Occupancy              Savannah Sparrow  Intercept -5.0307 1.0235 -7.3205 -4.9593 -3.0331 1.0052  742 -6.7879 -3.4024
## 84   Occupancy               Scarlet Tanager  Intercept  0.8502 0.3790  0.2052  0.8272  1.6605 1.0004 1492  0.2760  1.5027
## 85   Occupancy                  Song Sparrow  Intercept  0.2887 0.1933 -0.0885  0.2832  0.6764 1.0001 1200 -0.0293  0.6171
## 86   Occupancy                 Swamp Sparrow  Intercept -3.6221 0.5157 -4.7225 -3.5944 -2.6902 1.0117 1200 -4.5056 -2.8003
## 87   Occupancy             Tennessee Warbler  Intercept -5.8243 1.6636 -9.3059 -5.7092 -2.7516 1.0055  602 -8.7199 -3.1787
## 88   Occupancy                  Tree Swallow  Intercept -3.1204 0.5826 -4.2638 -3.1219 -1.8977 1.0001 1200 -4.0721 -2.1706
## 89   Occupancy               Tufted Titmouse  Intercept  3.1935 0.5845  2.3261  3.1203  4.6245 0.9999 1200  2.4271  4.2254
## 90   Occupancy                Turkey Vulture  Intercept -1.0948 1.0513 -2.8063 -1.2164  1.1005 1.0027  707 -2.5978  0.6554
## 91   Occupancy                         Veery  Intercept -1.8523 0.5756 -2.8320 -1.9106 -0.5464 1.0029 1090 -2.6558 -0.8698
## 92   Occupancy                 Virginia Rail  Intercept -5.7647 1.5659 -9.0737 -5.6851 -2.8961 1.0137  598 -8.2566 -3.3079
## 93   Occupancy                Warbling Vireo  Intercept -1.9453 0.2904 -2.5138 -1.9416 -1.4033 1.0027 1200 -2.4266 -1.4854
## 94   Occupancy       White-breasted Nuthatch  Intercept  2.8798 0.8356  1.7510  2.7197  4.9774 1.0048  864  1.8799  4.3641
## 95   Occupancy              White-eyed Vireo  Intercept -5.2500 1.0075 -7.6011 -5.1533 -3.5704 1.0095  992 -7.0540 -3.7932
## 96   Occupancy             Willow Flycatcher  Intercept -3.4582 0.5255 -4.5493 -3.4413 -2.5009 1.0077 1200 -4.3584 -2.6644
## 97   Occupancy                   Wild Turkey  Intercept -1.8149 1.6397 -3.9060 -2.2459  2.6282 1.0049  206 -3.6765  1.4591
## 98   Occupancy                   Winter Wren  Intercept -4.3014 0.9510 -6.3181 -4.2587 -2.3570 0.9997  922 -5.9249 -2.8223
## 99   Occupancy                     Wood Duck  Intercept -3.7399 1.1144 -5.8403 -3.7944 -1.4504 1.0005  683 -5.4959 -1.8909
## 100  Occupancy                   Wood Thrush  Intercept  0.9300 0.3428  0.3574  0.8951  1.6910 1.0018 1200  0.4280  1.5555
## 101  Occupancy          Yellow-billed Cuckoo  Intercept -1.6815 1.2099 -3.5389 -1.8751  1.2776 1.0222  414 -3.2934  0.5240
## 102  Occupancy                Yellow Warbler  Intercept -1.2739 0.2780 -1.8247 -1.2696 -0.7158 1.0239 1200 -1.7123 -0.8257
## 103  Occupancy         Yellow-throated Vireo  Intercept -1.5295 0.7001 -2.6394 -1.6010 -0.0648 1.0498  516 -2.4803 -0.3324
## 104  Occupancy       Yellow-throated Warbler  Intercept -3.0110 0.8095 -4.3727 -3.0940 -1.1220 1.0923  463 -4.1283 -1.6786
## 105  Occupancy            Acadian Flycatcher    tol_rel -1.2670 0.2554 -1.8211 -1.2630 -0.7882 1.0136 1200 -1.7145 -0.8670
## 106  Occupancy              Alder Flycatcher    tol_rel  0.5414 0.5286 -0.4509  0.5323  1.6032 1.0112 1200 -0.3114  1.4298
## 107  Occupancy                 American Crow    tol_rel  0.0961 0.2708 -0.3874  0.0920  0.6551 1.0005 1039 -0.3263  0.5278
## 108  Occupancy            American Goldfinch    tol_rel  0.1545 0.4167 -0.6296  0.1276  1.0502 1.0052 1200 -0.4957  0.8554
## 109  Occupancy              American Kestrel    tol_rel  0.1516 0.5274 -0.9475  0.1592  1.1174 1.0018 1255 -0.7433  0.9770
## 110  Occupancy             American Redstart    tol_rel  0.1130 0.3549 -0.5931  0.1215  0.8155 1.0029 1200 -0.4738  0.6924
## 111  Occupancy                American Robin    tol_rel  0.4606 0.3775 -0.1892  0.4344  1.2588 1.0069 1200 -0.0979  1.1412
## 112  Occupancy             American Woodcock    tol_rel  0.1691 0.4676 -0.7714  0.1614  1.0896 1.0007 1200 -0.6251  0.9405
## 113  Occupancy                    Barred Owl    tol_rel  0.6826 0.4796 -0.2426  0.6697  1.6775 1.0246 1088 -0.0880  1.4878
## 114  Occupancy                    Bald Eagle    tol_rel  0.2742 0.4664 -0.6259  0.2699  1.1750 1.0046 1200 -0.4722  1.0519
## 115  Occupancy                  Bank Swallow    tol_rel  0.8884 0.5075 -0.1351  0.8876  1.9091 1.0093 1200  0.0485  1.7054
## 116  Occupancy              Baltimore Oriole    tol_rel  0.7995 0.3008  0.2653  0.7754  1.4526 1.0137 1200  0.3394  1.2995
## 117  Occupancy                  Barn Swallow    tol_rel  0.4945 0.3851 -0.1749  0.4529  1.3502 1.0003 1200 -0.0786  1.1879
## 118  Occupancy        Black-capped Chickadee    tol_rel -0.3519 0.4550 -1.1947 -0.3703  0.5938 1.0006 1200 -1.0580  0.4313
## 119  Occupancy             Belted Kingfisher    tol_rel  0.2732 0.4003 -0.4453  0.2591  1.1741 1.0007 1737 -0.3325  0.9333
## 120  Occupancy         Blue-gray Gnatcatcher    tol_rel -0.4289 0.2634 -0.9594 -0.4286  0.0819 1.0036 1405 -0.8905 -0.0023
## 121  Occupancy          Brown-headed Cowbird    tol_rel  0.7477 0.3747  0.0936  0.7153  1.5608 1.0066 1200  0.2011  1.4142
## 122  Occupancy             Blue-headed Vireo    tol_rel  0.0169 0.5552 -1.0764  0.0042  1.1518 1.0014 1200 -0.8764  0.9272
## 123  Occupancy                      Blue Jay    tol_rel -0.3567 0.3075 -0.9244 -0.3669  0.2800 0.9993 1122 -0.8486  0.1537
## 124  Occupancy                      Bobolink    tol_rel  0.0893 0.5880 -1.0843  0.0989  1.2114 1.0036 1200 -0.9159  1.0304
## 125  Occupancy                 Brown Creeper    tol_rel -0.1026 0.3706 -0.8516 -0.0805  0.5804 1.0061 1200 -0.7364  0.4757
## 126  Occupancy                Brown Thrasher    tol_rel  1.2345 0.4631  0.4193  1.2022  2.2339 1.0138 1000  0.5369  2.0540
## 127  Occupancy  Black-throated Green Warbler    tol_rel  0.1039 0.5913 -1.0764  0.1195  1.1887 0.9997 1083 -0.8802  1.0479
## 128  Occupancy             Broad-winged Hawk    tol_rel -0.3274 0.5293 -1.4512 -0.3258  0.6361 0.9988 1200 -1.1858  0.4952
## 129  Occupancy           Blue-winged Warbler    tol_rel  0.6229 0.3931 -0.1336  0.6191  1.4077 1.0111 1322  0.0053  1.2972
## 130  Occupancy                  Canada Goose    tol_rel  0.5581 0.4584 -0.3270  0.5660  1.4830 1.0163 1303 -0.1636  1.2975
## 131  Occupancy                 Carolina Wren    tol_rel  0.6870 0.3190  0.1351  0.6652  1.3868 1.0024  965  0.2020  1.2583
## 132  Occupancy                 Cedar Waxwing    tol_rel  0.6381 0.2763  0.1442  0.6197  1.2042 1.0035 1200  0.2200  1.1194
## 133  Occupancy              Cerulean Warbler    tol_rel  0.1144 0.5777 -1.0815  0.1133  1.2456 1.0035 1200 -0.8486  1.0804
## 134  Occupancy              Chipping Sparrow    tol_rel  0.1979 0.2780 -0.3044  0.1904  0.8004 1.0051 1047 -0.2269  0.6762
## 135  Occupancy                 Chimney Swift    tol_rel -0.0221 0.3604 -0.6408 -0.0524  0.8215 1.0039 1087 -0.5591  0.6017
## 136  Occupancy                 Cliff Swallow    tol_rel  0.1352 0.5003 -0.8374  0.1410  1.1167 1.0149 1200 -0.7005  0.9271
## 137  Occupancy                Common Grackle    tol_rel  0.5610 0.3595 -0.0856  0.5212  1.3254 1.0000 1200  0.0289  1.2129
## 138  Occupancy                 Cooper's Hawk    tol_rel  0.4542 0.3582 -0.2098  0.4508  1.1609 1.0012 1183 -0.1260  1.0215
## 139  Occupancy           Common Yellowthroat    tol_rel  0.6847 0.2277  0.2617  0.6820  1.1378 1.0126 1200  0.3139  1.0551
## 140  Occupancy               Dark-eyed Junco    tol_rel -0.5121 0.3671 -1.2833 -0.4941  0.1658 1.0010 1200 -1.1635  0.0639
## 141  Occupancy              Downy Woodpecker    tol_rel  0.1319 0.3389 -0.5167  0.1268  0.8379 1.0027 1200 -0.4197  0.7155
## 142  Occupancy              Eastern Bluebird    tol_rel  0.3175 0.3067 -0.2618  0.3064  0.9542 1.0080 1303 -0.1646  0.8147
## 143  Occupancy              Eastern Kingbird    tol_rel  0.7866 0.3405  0.1518  0.7902  1.4546 1.0009 1200  0.2344  1.3336
## 144  Occupancy            Eastern Meadowlark    tol_rel  0.0178 0.5002 -0.9925  0.0353  0.9746 1.0019 1402 -0.8769  0.8457
## 145  Occupancy                Eastern Phoebe    tol_rel -0.4941 0.3334 -1.2009 -0.4765  0.1362 1.0029 1200 -1.0777  0.0183
## 146  Occupancy                Eastern Towhee    tol_rel  0.6125 0.2599  0.1179  0.6130  1.1116 1.0017 1200  0.1938  1.0457
## 147  Occupancy            Eastern Wood-Pewee    tol_rel -0.9553 0.2886 -1.5293 -0.9437 -0.4296 1.0024 1200 -1.4493 -0.5185
## 148  Occupancy             European Starling    tol_rel  0.7028 0.2633  0.2174  0.6972  1.2500 1.0046 1309  0.2895  1.1391
## 149  Occupancy                 Field Sparrow    tol_rel  0.6494 0.2912  0.1061  0.6488  1.2622 1.0114 1200  0.1849  1.1392
## 150  Occupancy              Great Blue Heron    tol_rel  0.1328 0.3839 -0.6008  0.1207  0.9384 1.0003 1200 -0.4727  0.7740
## 151  Occupancy      Great Crested Flycatcher    tol_rel -0.3814 0.4395 -1.1168 -0.4332  0.6206 1.0059 1038 -1.0154  0.3926
## 152  Occupancy              Great Horned Owl    tol_rel  0.1382 0.5606 -1.0407  0.1533  1.2142 1.0033 1200 -0.7900  1.0220
## 153  Occupancy                  Gray Catbird    tol_rel  0.7737 0.2282  0.3460  0.7655  1.2504 1.0152 1200  0.4025  1.1446
## 154  Occupancy                   Green Heron    tol_rel  0.2794 0.5395 -0.7984  0.2878  1.3336 1.0072  926 -0.5905  1.1518
## 155  Occupancy              Hairy Woodpecker    tol_rel -0.6512 0.4107 -1.3630 -0.6836  0.2942 1.0093 1037 -1.2571  0.0669
## 156  Occupancy                  Herring Gull    tol_rel -0.1570 0.5274 -1.2734 -0.1432  0.8262 1.0082 1200 -1.0430  0.6633
## 157  Occupancy                 Hermit Thrush    tol_rel -0.2313 0.5304 -1.3161 -0.2013  0.7367 1.0008 1125 -1.1419  0.5714
## 158  Occupancy                   House Finch    tol_rel  0.1867 0.3794 -0.5222  0.1835  0.9696 1.0064 1200 -0.4257  0.8583
## 159  Occupancy                 House Sparrow    tol_rel  0.1886 0.2489 -0.2751  0.1877  0.6769 1.0006 1200 -0.2189  0.5916
## 160  Occupancy                Hooded Warbler    tol_rel -0.4268 0.2467 -0.9264 -0.4218  0.0352 1.0029 1200 -0.8436 -0.0441
## 161  Occupancy                    House Wren    tol_rel  0.2119 0.1894 -0.1538  0.2111  0.5748 1.0018 1200 -0.1031  0.5201
## 162  Occupancy                Indigo Bunting    tol_rel  0.3765 0.2106 -0.0073  0.3668  0.8026 1.0051 1126  0.0510  0.7311
## 163  Occupancy                      Killdeer    tol_rel  0.7528 0.3536  0.1175  0.7381  1.5137 1.0042 1200  0.2015  1.3474
## 164  Occupancy         Louisiana Waterthrush    tol_rel -0.0751 0.3531 -0.7426 -0.0709  0.6110 1.0041 1200 -0.6482  0.5010
## 165  Occupancy                       Mallard    tol_rel  0.1938 0.4228 -0.6138  0.1756  1.0424 1.0005 1008 -0.4873  0.8779
## 166  Occupancy                 Mourning Dove    tol_rel  0.9647 0.3389  0.3349  0.9414  1.6842 1.0026 1081  0.4347  1.5198
## 167  Occupancy             Northern Cardinal    tol_rel  0.4414 0.3516 -0.2417  0.4312  1.1762 1.0061 1200 -0.1279  1.0347
## 168  Occupancy              Northern Flicker    tol_rel  0.2780 0.4838 -0.6390  0.2508  1.3194 1.0088 1200 -0.4667  1.1075
## 169  Occupancy               Northern Parula    tol_rel -0.2899 0.5337 -1.3744 -0.2888  0.7395 1.0098 1200 -1.2023  0.5626
## 170  Occupancy Northern Rough-winged Swallow    tol_rel  0.5697 0.3802 -0.0956  0.5517  1.4002 1.0014 1200  0.0031  1.2491
## 171  Occupancy                Orchard Oriole    tol_rel  0.9950 0.3273  0.4139  0.9761  1.6756 1.0082 1200  0.4956  1.5615
## 172  Occupancy                      Ovenbird    tol_rel -0.1736 0.3451 -0.8392 -0.1761  0.4643 1.0015 1327 -0.7380  0.3719
## 173  Occupancy           Pileated Woodpecker    tol_rel -0.2246 0.4444 -1.0145 -0.2492  0.7505 1.0108 1200 -0.8767  0.5647
## 174  Occupancy                  Purple Finch    tol_rel  0.5913 0.5095 -0.3599  0.5913  1.6102 1.0079 1200 -0.2166  1.4008
## 175  Occupancy                 Purple Martin    tol_rel  0.1103 0.5899 -1.0359  0.1084  1.3139 1.0177  657 -0.8463  1.0976
## 176  Occupancy        Rose-breasted Grosbeak    tol_rel  0.1737 0.3002 -0.3701  0.1577  0.8031 1.0020 1312 -0.2872  0.6804
## 177  Occupancy              Ring-billed Gull    tol_rel  0.2630 0.3367 -0.3649  0.2614  0.9057 1.0024 1425 -0.2993  0.8267
## 178  Occupancy         Red-breasted Nuthatch    tol_rel  0.1318 0.5268 -0.9594  0.1235  1.1438 1.0010 1200 -0.7384  0.9946
## 179  Occupancy        Red-bellied Woodpecker    tol_rel -0.6218 0.3870 -1.3384 -0.6376  0.2258 1.0047 1330 -1.2337  0.0583
## 180  Occupancy                Red-eyed Vireo    tol_rel -1.0215 0.2796 -1.5891 -1.0223 -0.4775 1.0138 1200 -1.4693 -0.5763
## 181  Occupancy         Red-headed Woodpecker    tol_rel -0.3260 0.4512 -1.2448 -0.3179  0.5301 1.0006 1200 -1.0926  0.3589
## 182  Occupancy                   Rock Pigeon    tol_rel -0.0222 0.5085 -0.9591 -0.0201  1.0303 1.0006 1219 -0.8223  0.8074
## 183  Occupancy           Red-shouldered Hawk    tol_rel -0.0181 0.5290 -1.0253 -0.0472  1.0933 1.0107 1299 -0.8535  0.9228
## 184  Occupancy               Red-tailed Hawk    tol_rel  0.3683 0.4100 -0.3798  0.3504  1.2605 1.0035 1200 -0.2622  1.0576
## 185  Occupancy     Ruby-throated Hummingbird    tol_rel  0.2975 0.5197 -0.6989  0.2817  1.3295 1.0009  910 -0.5450  1.1259
## 186  Occupancy          Red-winged Blackbird    tol_rel  0.7366 0.2176  0.3237  0.7371  1.1623 1.0031 1200  0.3927  1.0956
## 187  Occupancy              Savannah Sparrow    tol_rel  0.1466 0.5268 -0.8281  0.1406  1.1530 1.0059 1200 -0.6988  1.0162
## 188  Occupancy               Scarlet Tanager    tol_rel -1.0621 0.2875 -1.6177 -1.0583 -0.5001 1.0144 1200 -1.5407 -0.5923
## 189  Occupancy                  Song Sparrow    tol_rel  0.7664 0.2267  0.3510  0.7470  1.2424 1.0181 1200  0.4152  1.1563
## 190  Occupancy                 Swamp Sparrow    tol_rel  0.3745 0.3479 -0.3294  0.3761  1.0958 1.0015 1200 -0.1990  0.9525
## 191  Occupancy             Tennessee Warbler    tol_rel  0.1052 0.6137 -1.0864  0.1125  1.3293 1.0030 1468 -0.8847  1.1023
## 192  Occupancy                  Tree Swallow    tol_rel  0.8699 0.3310  0.2338  0.8647  1.5067 1.0002 1200  0.3262  1.4360
## 193  Occupancy               Tufted Titmouse    tol_rel -0.5437 0.3649 -1.2491 -0.5455  0.1863 1.0014 1345 -1.1205  0.0496
## 194  Occupancy                Turkey Vulture    tol_rel  0.7207 0.4782 -0.1060  0.7016  1.7600 1.0039 1161 -0.0152  1.5705
## 195  Occupancy                         Veery    tol_rel  0.0346 0.3387 -0.6287  0.0420  0.6657 1.0028 1010 -0.5252  0.5681
## 196  Occupancy                 Virginia Rail    tol_rel  0.1173 0.5640 -0.9531  0.1032  1.2074 1.0027 1200 -0.7741  1.0661
## 197  Occupancy                Warbling Vireo    tol_rel  0.6796 0.2483  0.1965  0.6797  1.1796 1.0096 1200  0.2842  1.0820
## 198  Occupancy       White-breasted Nuthatch    tol_rel -0.4994 0.4206 -1.2539 -0.5215  0.3981 0.9993  922 -1.1468  0.2135
## 199  Occupancy              White-eyed Vireo    tol_rel -0.1036 0.5513 -1.1959 -0.0918  0.9190 0.9993 1200 -1.0177  0.7958
## 200  Occupancy             Willow Flycatcher    tol_rel  1.1755 0.3431  0.5352  1.1844  1.8488 1.0041 1258  0.6153  1.7406
## 201  Occupancy                   Wild Turkey    tol_rel -0.4356 0.5231 -1.4361 -0.4276  0.5772 1.0000 1009 -1.2827  0.4037
## 202  Occupancy                   Winter Wren    tol_rel -0.3672 0.5249 -1.3946 -0.3597  0.6823 1.0010 1200 -1.2837  0.4841
## 203  Occupancy                     Wood Duck    tol_rel  0.4306 0.4888 -0.5067  0.4160  1.4379 1.0053 1200 -0.3246  1.2313
## 204  Occupancy                   Wood Thrush    tol_rel -0.4867 0.2349 -0.9682 -0.4843 -0.0378 1.0010 1303 -0.8794 -0.1037
## 205  Occupancy          Yellow-billed Cuckoo    tol_rel  0.0335 0.4326 -0.7772  0.0392  0.8762 1.0040 1419 -0.6495  0.7351
## 206  Occupancy                Yellow Warbler    tol_rel  1.0415 0.2664  0.5592  1.0343  1.5889 1.0087 1200  0.6218  1.5096
## 207  Occupancy         Yellow-throated Vireo    tol_rel -0.5708 0.3969 -1.3641 -0.5458  0.1663 1.0091 1200 -1.2684  0.0614
## 208  Occupancy       Yellow-throated Warbler    tol_rel -0.0377 0.4213 -0.9002 -0.0232  0.7962 1.0078 1311 -0.7313  0.6493
## 209  Occupancy            Acadian Flycatcher        svp  0.7480 0.2548  0.2699  0.7420  1.2939 1.0117 1200  0.3332  1.1939
## 210  Occupancy              Alder Flycatcher        svp  0.0024 0.3983 -0.8050  0.0017  0.7897 1.0034 1200 -0.6513  0.6538
## 211  Occupancy                 American Crow        svp  0.0301 0.2371 -0.3992  0.0183  0.5281 1.0025 1200 -0.3335  0.4307
## 212  Occupancy            American Goldfinch        svp  0.0868 0.3255 -0.5172  0.0831  0.7418 1.0028 1200 -0.4395  0.6499
## 213  Occupancy              American Kestrel        svp -0.1772 0.3951 -0.9626 -0.1758  0.5936 1.0079 1094 -0.8485  0.4630
## 214  Occupancy             American Redstart        svp -0.1066 0.3057 -0.7668 -0.0946  0.4697 1.0042  990 -0.6115  0.3587
## 215  Occupancy                American Robin        svp -0.4572 0.2388 -0.9239 -0.4524 -0.0352 1.0086 1200 -0.8490 -0.0957
## 216  Occupancy             American Woodcock        svp -0.1056 0.3857 -0.9092 -0.1052  0.6399 1.0020 1200 -0.7557  0.5217
## 217  Occupancy                    Barred Owl        svp  0.1185 0.3816 -0.6230  0.1321  0.8959 1.0019 1200 -0.5222  0.7525
## 218  Occupancy                    Bald Eagle        svp -0.2531 0.3934 -1.0899 -0.2417  0.4770 1.0143 1200 -0.9609  0.3410
## 219  Occupancy                  Bank Swallow        svp -0.0317 0.3878 -0.7831 -0.0421  0.7397 1.0087 1200 -0.6638  0.6187
## 220  Occupancy              Baltimore Oriole        svp -0.5242 0.2534 -1.0560 -0.5223 -0.0719 1.0039 1200 -0.9505 -0.1286
## 221  Occupancy                  Barn Swallow        svp -0.1890 0.3392 -0.8124 -0.2010  0.4652 1.0032 1200 -0.7300  0.3646
## 222  Occupancy        Black-capped Chickadee        svp  0.1418 0.3910 -0.6268  0.1375  0.9551 0.9999 1103 -0.4781  0.8061
## 223  Occupancy             Belted Kingfisher        svp -0.2603 0.3281 -0.9056 -0.2545  0.3618 1.0003 1200 -0.8240  0.2571
## 224  Occupancy         Blue-gray Gnatcatcher        svp  0.2565 0.3121 -0.3196  0.2353  0.9125 1.0082 1200 -0.2332  0.8039
## 225  Occupancy          Brown-headed Cowbird        svp  0.1072 0.2758 -0.3723  0.0979  0.7133 1.0025 1200 -0.3227  0.5788
## 226  Occupancy             Blue-headed Vireo        svp -0.0038 0.3814 -0.7451 -0.0092  0.7445 1.0010 1200 -0.6370  0.6343
## 227  Occupancy                      Blue Jay        svp -0.1111 0.2615 -0.6382 -0.1080  0.4051 1.0009 1200 -0.5372  0.3137
## 228  Occupancy                      Bobolink        svp -0.0591 0.4372 -0.9794 -0.0585  0.7910 1.0198 1200 -0.7415  0.6478
## 229  Occupancy                 Brown Creeper        svp  0.6037 0.2755  0.0703  0.5956  1.1460 1.0066 1200  0.1622  1.0400
## 230  Occupancy                Brown Thrasher        svp -0.1698 0.3838 -0.9380 -0.1739  0.6423 1.0317 1160 -0.8013  0.4737
## 231  Occupancy  Black-throated Green Warbler        svp -0.0824 0.4104 -0.9031 -0.0744  0.7134 0.9991 1089 -0.7612  0.5747
## 232  Occupancy             Broad-winged Hawk        svp  0.2436 0.3581 -0.4322  0.2351  0.9526 1.0107 1200 -0.3490  0.8392
## 233  Occupancy           Blue-winged Warbler        svp -0.0377 0.3326 -0.6882 -0.0358  0.5867 0.9991 1424 -0.5659  0.5100
## 234  Occupancy                  Canada Goose        svp -0.2379 0.3608 -0.9610 -0.2344  0.4926 1.0042 1200 -0.8388  0.3808
## 235  Occupancy                 Carolina Wren        svp  0.2682 0.2416 -0.2000  0.2655  0.7537 1.0025 2477 -0.1272  0.6755
## 236  Occupancy                 Cedar Waxwing        svp -0.3019 0.2589 -0.8431 -0.2857  0.1778 1.0156 1200 -0.7383  0.0971
## 237  Occupancy              Cerulean Warbler        svp -0.0532 0.4080 -0.8574 -0.0448  0.7653 1.0043 1200 -0.7142  0.6129
## 238  Occupancy              Chipping Sparrow        svp  0.0733 0.2570 -0.4197  0.0608  0.5937 1.0053  952 -0.3363  0.5203
## 239  Occupancy                 Chimney Swift        svp -0.2491 0.2794 -0.8055 -0.2525  0.3199 1.0237  967 -0.6940  0.2272
## 240  Occupancy                 Cliff Swallow        svp -0.1635 0.3983 -0.9580 -0.1491  0.6128 1.0030 1200 -0.8070  0.4694
## 241  Occupancy                Common Grackle        svp -0.2012 0.2671 -0.7203 -0.1934  0.3329 1.0077 1200 -0.6434  0.2265
## 242  Occupancy                 Cooper's Hawk        svp  0.0846 0.3256 -0.5962  0.0890  0.6809 1.0013 1200 -0.4585  0.5802
## 243  Occupancy           Common Yellowthroat        svp  0.0584 0.2172 -0.3616  0.0587  0.4812 1.0048  963 -0.3063  0.4075
## 244  Occupancy               Dark-eyed Junco        svp  0.6843 0.2815  0.1666  0.6701  1.2609 1.0139 1207  0.2349  1.1886
## 245  Occupancy              Downy Woodpecker        svp  0.1239 0.3316 -0.4944  0.1026  0.8191 1.0047 1200 -0.3928  0.7245
## 246  Occupancy              Eastern Bluebird        svp  0.3416 0.2792 -0.2007  0.3426  0.8929 1.0038 1200 -0.0984  0.7962
## 247  Occupancy              Eastern Kingbird        svp  0.0390 0.3186 -0.5748  0.0440  0.6865 1.0101 1200 -0.4754  0.5454
## 248  Occupancy            Eastern Meadowlark        svp -0.1465 0.3758 -0.9090 -0.1412  0.5959 1.0052 1392 -0.7628  0.4671
## 249  Occupancy                Eastern Phoebe        svp -0.0485 0.2647 -0.5750 -0.0496  0.4823 1.0007 1200 -0.4790  0.3741
## 250  Occupancy                Eastern Towhee        svp -0.1521 0.2428 -0.6290 -0.1492  0.3256 1.0086 1304 -0.5514  0.2433
## 251  Occupancy            Eastern Wood-Pewee        svp  0.0213 0.3122 -0.5726  0.0060  0.6522 0.9996 1200 -0.4822  0.5498
## 252  Occupancy             European Starling        svp -0.5856 0.3034 -1.2370 -0.5755 -0.0308 1.0007 1200 -1.1202 -0.1055
## 253  Occupancy                 Field Sparrow        svp -0.2141 0.2993 -0.8215 -0.2105  0.3758 1.0064  964 -0.7014  0.2797
## 254  Occupancy              Great Blue Heron        svp -0.0801 0.3207 -0.6899 -0.0766  0.5439 1.0092 1200 -0.5967  0.4601
## 255  Occupancy      Great Crested Flycatcher        svp  0.0829 0.3522 -0.6077  0.0802  0.8046 1.0017 1200 -0.4778  0.6784
## 256  Occupancy              Great Horned Owl        svp -0.0898 0.3929 -0.8622 -0.1007  0.6867 1.0165 1200 -0.7379  0.5539
## 257  Occupancy                  Gray Catbird        svp -0.4241 0.2120 -0.8403 -0.4161 -0.0346 1.0064 1200 -0.7641 -0.0937
## 258  Occupancy                   Green Heron        svp -0.0993 0.3940 -0.8597 -0.0954  0.6519 0.9994 1200 -0.7563  0.5158
## 259  Occupancy              Hairy Woodpecker        svp  0.0317 0.3620 -0.6378  0.0106  0.7722 1.0042 1200 -0.5221  0.6423
## 260  Occupancy                  Herring Gull        svp -0.1858 0.3852 -0.9646 -0.1832  0.5649 1.0024  863 -0.8311  0.4366
## 261  Occupancy                 Hermit Thrush        svp  0.3009 0.3628 -0.3848  0.2906  1.0253 1.0051 1200 -0.2823  0.8986
## 262  Occupancy                   House Finch        svp -0.6101 0.3374 -1.2973 -0.6018  0.0220 1.0069 1200 -1.1541 -0.0702
## 263  Occupancy                 House Sparrow        svp -0.8296 0.3148 -1.4863 -0.8249 -0.2455 1.0090 1200 -1.3587 -0.3228
## 264  Occupancy                Hooded Warbler        svp  0.4001 0.2187 -0.0147  0.3948  0.8393 1.0004 1200  0.0577  0.7687
## 265  Occupancy                    House Wren        svp -0.3120 0.1978 -0.7035 -0.3069  0.0579 1.0048 1200 -0.6583  0.0074
## 266  Occupancy                Indigo Bunting        svp -0.1614 0.2039 -0.5838 -0.1597  0.2174 1.0026 1200 -0.5034  0.1798
## 267  Occupancy                      Killdeer        svp -0.3518 0.3349 -1.0142 -0.3540  0.2790 1.0162 1200 -0.9134  0.1811
## 268  Occupancy         Louisiana Waterthrush        svp  0.0085 0.2830 -0.5282  0.0076  0.5488 1.0148 1200 -0.4551  0.4704
## 269  Occupancy                       Mallard        svp -0.3376 0.3708 -1.0700 -0.3294  0.3907 1.0003 1200 -0.9417  0.2355
## 270  Occupancy                 Mourning Dove        svp -0.0720 0.2742 -0.6151 -0.0717  0.4661 1.0064 1200 -0.5283  0.3929
## 271  Occupancy             Northern Cardinal        svp  0.0374 0.2863 -0.5173  0.0405  0.6332 1.0160 1776 -0.4195  0.5093
## 272  Occupancy              Northern Flicker        svp -0.1613 0.3181 -0.7417 -0.1839  0.5020 1.0208 1200 -0.6563  0.3918
## 273  Occupancy               Northern Parula        svp -0.1981 0.4012 -1.0021 -0.1644  0.5459 0.9998 1210 -0.8716  0.4141
## 274  Occupancy Northern Rough-winged Swallow        svp -0.2405 0.3403 -0.9180 -0.2298  0.4002 1.0013 1200 -0.7962  0.2954
## 275  Occupancy                Orchard Oriole        svp -0.1568 0.3199 -0.8034 -0.1564  0.4665 1.0063 1084 -0.6892  0.3620
## 276  Occupancy                      Ovenbird        svp  0.1195 0.2790 -0.4598  0.1264  0.6329 1.0003 1200 -0.3401  0.5547
## 277  Occupancy           Pileated Woodpecker        svp  0.2084 0.3568 -0.4807  0.2130  0.9351 1.0034 1200 -0.3676  0.8167
## 278  Occupancy                  Purple Finch        svp  0.0263 0.3898 -0.7469  0.0251  0.7622 1.0013 1200 -0.6265  0.6535
## 279  Occupancy                 Purple Martin        svp -0.0476 0.4184 -0.8758 -0.0422  0.7565 1.0028 1200 -0.7446  0.6165
## 280  Occupancy        Rose-breasted Grosbeak        svp -0.3316 0.2925 -0.9331 -0.3234  0.2109 1.0099 1200 -0.8014  0.1180
## 281  Occupancy              Ring-billed Gull        svp -0.0612 0.3226 -0.7103 -0.0537  0.5786 1.0024 1056 -0.5867  0.4406
## 282  Occupancy         Red-breasted Nuthatch        svp -0.0900 0.3989 -0.8639 -0.0725  0.6679 0.9996 1200 -0.7773  0.5727
## 283  Occupancy        Red-bellied Woodpecker        svp  0.0681 0.3233 -0.5659  0.0673  0.6946 1.0029 1200 -0.4665  0.6057
## 284  Occupancy                Red-eyed Vireo        svp  0.2669 0.3290 -0.3311  0.2482  0.9808 1.0066 1200 -0.2509  0.8381
## 285  Occupancy         Red-headed Woodpecker        svp -0.4592 0.3695 -1.2189 -0.4314  0.2096 1.0202 1200 -1.0943  0.1110
## 286  Occupancy                   Rock Pigeon        svp -0.2695 0.4012 -1.0841 -0.2532  0.4526 1.0056 1095 -0.9673  0.3675
## 287  Occupancy           Red-shouldered Hawk        svp -0.2639 0.3615 -0.9671 -0.2525  0.4540 1.0020 1200 -0.8482  0.3312
## 288  Occupancy               Red-tailed Hawk        svp -0.1989 0.3478 -0.8806 -0.1872  0.4860 1.0037 1125 -0.7684  0.3800
## 289  Occupancy     Ruby-throated Hummingbird        svp  0.0022 0.3620 -0.7341 -0.0008  0.7543 1.0087 1103 -0.5870  0.6157
## 290  Occupancy          Red-winged Blackbird        svp -0.2647 0.2325 -0.7343 -0.2576  0.1791 1.0005 1200 -0.6570  0.1101
## 291  Occupancy              Savannah Sparrow        svp -0.1782 0.3998 -0.9546 -0.1632  0.5943 1.0006 1200 -0.8260  0.4552
## 292  Occupancy               Scarlet Tanager        svp  0.3601 0.2860 -0.1814  0.3514  0.9615 1.0004 1200 -0.0893  0.8657
## 293  Occupancy                  Song Sparrow        svp -0.1791 0.1827 -0.5312 -0.1816  0.1672 1.0088 1200 -0.4769  0.1108
## 294  Occupancy                 Swamp Sparrow        svp -0.1393 0.3267 -0.8031 -0.1387  0.4733 1.0078 1200 -0.7040  0.3924
## 295  Occupancy             Tennessee Warbler        svp -0.0639 0.4119 -0.8645 -0.0796  0.7442 1.0075 1551 -0.7123  0.6249
## 296  Occupancy                  Tree Swallow        svp -0.0956 0.3324 -0.7681 -0.0983  0.5574 1.0181 1200 -0.6419  0.4326
## 297  Occupancy               Tufted Titmouse        svp  0.1721 0.3303 -0.4547  0.1719  0.8265 1.0137 1200 -0.3572  0.7156
## 298  Occupancy                Turkey Vulture        svp -0.4063 0.3767 -1.1664 -0.4006  0.3523 1.0140 1271 -1.0285  0.1919
## 299  Occupancy                         Veery        svp  0.2288 0.2703 -0.2766  0.2153  0.8044 1.0056 1200 -0.1871  0.6946
## 300  Occupancy                 Virginia Rail        svp -0.0712 0.4108 -0.8426 -0.0701  0.7098 1.0029 1200 -0.7251  0.6211
## 301  Occupancy                Warbling Vireo        svp -0.4477 0.2734 -0.9787 -0.4449  0.0770 1.0033 1200 -0.9027 -0.0128
## 302  Occupancy       White-breasted Nuthatch        svp  0.1087 0.3552 -0.5802  0.1159  0.8125 1.0059 1200 -0.4518  0.6819
## 303  Occupancy              White-eyed Vireo        svp -0.1477 0.3917 -0.9407 -0.1427  0.6028 1.0033 1200 -0.8101  0.4894
## 304  Occupancy             Willow Flycatcher        svp -0.0779 0.3299 -0.7590 -0.0633  0.5488 1.0012 1200 -0.6631  0.4366
## 305  Occupancy                   Wild Turkey        svp -0.0709 0.3471 -0.7590 -0.0637  0.6255 1.0013 1200 -0.6422  0.5148
## 306  Occupancy                   Winter Wren        svp  0.3528 0.3665 -0.3862  0.3651  1.0928 1.0000 1037 -0.2526  0.9286
## 307  Occupancy                     Wood Duck        svp -0.1889 0.3873 -0.9891 -0.1763  0.5294 1.0034 1200 -0.8553  0.4485
## 308  Occupancy                   Wood Thrush        svp  0.1635 0.2788 -0.3450  0.1457  0.7514 1.0245 1200 -0.2735  0.6265
## 309  Occupancy          Yellow-billed Cuckoo        svp  0.3737 0.3395 -0.2797  0.3611  1.0492 1.0051 1200 -0.1799  0.9399
## 310  Occupancy                Yellow Warbler        svp -0.3269 0.2428 -0.7995 -0.3282  0.1476 1.0206 1200 -0.7158  0.0725
## 311  Occupancy         Yellow-throated Vireo        svp  0.3317 0.2876 -0.2200  0.3124  0.8998 1.0114 1200 -0.1431  0.8138
## 312  Occupancy       Yellow-throated Warbler        svp -0.0855 0.3450 -0.7775 -0.0776  0.5515 1.0187 1200 -0.6878  0.4730
## 313  Occupancy            Acadian Flycatcher      dicot  0.3787 0.2011 -0.0029  0.3729  0.8148 1.0096 1308  0.0626  0.7072
## 314  Occupancy              Alder Flycatcher      dicot  0.1628 0.2659 -0.3856  0.1752  0.6784 1.0019 1185 -0.2959  0.5845
## 315  Occupancy                 American Crow      dicot  0.1766 0.2030 -0.2236  0.1817  0.5671 1.0047 1200 -0.1610  0.4902
## 316  Occupancy            American Goldfinch      dicot  0.2214 0.2571 -0.2821  0.2225  0.7143 1.0011 1200 -0.2060  0.6543
## 317  Occupancy              American Kestrel      dicot  0.2625 0.2635 -0.2203  0.2596  0.7997 1.0065 1310 -0.1511  0.6882
## 318  Occupancy             American Redstart      dicot  0.2381 0.2379 -0.2422  0.2365  0.7044 0.9994 1194 -0.1615  0.6236
## 319  Occupancy                American Robin      dicot  0.0464 0.2323 -0.4153  0.0434  0.5102 1.0103 1200 -0.3429  0.4294
## 320  Occupancy             American Woodcock      dicot  0.1721 0.2632 -0.3607  0.1817  0.6703 1.0030 1200 -0.2803  0.5943
## 321  Occupancy                    Barred Owl      dicot  0.1349 0.2649 -0.3745  0.1427  0.6377 1.0003 1200 -0.3188  0.5729
## 322  Occupancy                    Bald Eagle      dicot  0.1890 0.2725 -0.3538  0.1969  0.7126 1.0086 1200 -0.2532  0.6219
## 323  Occupancy                  Bank Swallow      dicot  0.1812 0.2629 -0.3458  0.1818  0.6898 1.0054 1200 -0.2498  0.5738
## 324  Occupancy              Baltimore Oriole      dicot  0.4607 0.2226  0.0516  0.4492  0.9319 1.0007 1200  0.1069  0.8371
## 325  Occupancy                  Barn Swallow      dicot  0.5202 0.2356  0.0748  0.5117  0.9866 1.0159 1200  0.1363  0.9178
## 326  Occupancy        Black-capped Chickadee      dicot  0.2552 0.2668 -0.2605  0.2603  0.7982 1.0187 1200 -0.1797  0.6935
## 327  Occupancy             Belted Kingfisher      dicot  0.3072 0.2583 -0.1776  0.3008  0.8440 1.0032 1200 -0.0931  0.7517
## 328  Occupancy         Blue-gray Gnatcatcher      dicot  0.3756 0.2358 -0.0466  0.3642  0.8863 1.0046 1200  0.0085  0.8049
## 329  Occupancy          Brown-headed Cowbird      dicot  0.4658 0.2594 -0.0182  0.4532  1.0324 1.0060 1100  0.0689  0.9204
## 330  Occupancy             Blue-headed Vireo      dicot  0.2574 0.2660 -0.2705  0.2588  0.8090 1.0169  884 -0.1690  0.6967
## 331  Occupancy                      Blue Jay      dicot -0.0202 0.2508 -0.5376 -0.0202  0.4599 1.0213 1200 -0.4481  0.3836
## 332  Occupancy                      Bobolink      dicot  0.2452 0.2895 -0.3152  0.2376  0.8147 1.0021 1200 -0.2215  0.7305
## 333  Occupancy                 Brown Creeper      dicot  0.3606 0.2292 -0.0763  0.3468  0.8229 1.0025 1200 -0.0043  0.7534
## 334  Occupancy                Brown Thrasher      dicot  0.2305 0.2627 -0.2995  0.2276  0.7469 1.0063 1200 -0.2135  0.6480
## 335  Occupancy  Black-throated Green Warbler      dicot  0.2344 0.2760 -0.3205  0.2337  0.7975 1.0018 1200 -0.2136  0.6961
## 336  Occupancy             Broad-winged Hawk      dicot  0.2649 0.2608 -0.2699  0.2661  0.7702 1.0039 1200 -0.1511  0.6805
## 337  Occupancy           Blue-winged Warbler      dicot  0.2456 0.2390 -0.2107  0.2443  0.7507 1.0037 1200 -0.1328  0.6452
## 338  Occupancy                  Canada Goose      dicot  0.2451 0.2575 -0.2810  0.2430  0.7624 1.0114 1084 -0.1759  0.6632
## 339  Occupancy                 Carolina Wren      dicot  0.2032 0.2265 -0.2451  0.2012  0.6566 1.0018 1200 -0.1587  0.5622
## 340  Occupancy                 Cedar Waxwing      dicot  0.2074 0.2038 -0.1759  0.2068  0.6129 1.0297 1200 -0.1149  0.5542
## 341  Occupancy              Cerulean Warbler      dicot  0.2390 0.2728 -0.2972  0.2413  0.7895 1.0083 1200 -0.2063  0.6899
## 342  Occupancy              Chipping Sparrow      dicot  0.2250 0.2190 -0.1682  0.2258  0.6310 1.0225 1200 -0.1280  0.5730
## 343  Occupancy                 Chimney Swift      dicot  0.2539 0.2296 -0.1882  0.2452  0.6912 1.0031 1200 -0.1036  0.6215
## 344  Occupancy                 Cliff Swallow      dicot  0.1757 0.2592 -0.3524  0.1847  0.6733 1.0007 1200 -0.2550  0.5860
## 345  Occupancy                Common Grackle      dicot  0.0275 0.2375 -0.4561  0.0380  0.4629 1.0054 1200 -0.3804  0.4034
## 346  Occupancy                 Cooper's Hawk      dicot  0.0707 0.2435 -0.4176  0.0749  0.5374 1.0010 1329 -0.3263  0.4606
## 347  Occupancy           Common Yellowthroat      dicot  0.4056 0.1949  0.0485  0.4010  0.8130 1.0003 1200  0.0921  0.7200
## 348  Occupancy               Dark-eyed Junco      dicot  0.0609 0.2290 -0.3990  0.0688  0.4957 1.0046 1240 -0.3197  0.4090
## 349  Occupancy              Downy Woodpecker      dicot  0.2670 0.2546 -0.2329  0.2694  0.7943 1.0061 1200 -0.1500  0.6832
## 350  Occupancy              Eastern Bluebird      dicot  0.1786 0.2477 -0.3025  0.1829  0.6562 1.0076 1089 -0.2294  0.5711
## 351  Occupancy              Eastern Kingbird      dicot  0.4184 0.2348 -0.0174  0.4064  0.8911 1.0035 1200  0.0441  0.8213
## 352  Occupancy            Eastern Meadowlark      dicot  0.4170 0.2558 -0.0379  0.4028  0.9573 1.0010 1200  0.0298  0.8558
## 353  Occupancy                Eastern Phoebe      dicot  0.2776 0.2234 -0.1423  0.2748  0.7314 1.0000 1200 -0.0821  0.6408
## 354  Occupancy                Eastern Towhee      dicot  0.5091 0.2092  0.1214  0.5016  0.9290 1.0345 1200  0.1718  0.8680
## 355  Occupancy            Eastern Wood-Pewee      dicot  0.3527 0.2378 -0.0957  0.3455  0.8381 1.0050 1200 -0.0270  0.7386
## 356  Occupancy             European Starling      dicot  0.2244 0.2246 -0.2142  0.2280  0.6584 1.0086 1278 -0.1447  0.5972
## 357  Occupancy                 Field Sparrow      dicot  0.2233 0.2255 -0.2251  0.2195  0.6539 1.0052 1200 -0.1405  0.5938
## 358  Occupancy              Great Blue Heron      dicot  0.0715 0.2486 -0.4408  0.0755  0.5261 1.0007 1200 -0.3544  0.4685
## 359  Occupancy      Great Crested Flycatcher      dicot  0.2278 0.2563 -0.2812  0.2239  0.7553 1.0013 1200 -0.1727  0.6577
## 360  Occupancy              Great Horned Owl      dicot  0.2884 0.2618 -0.2434  0.2761  0.8188 1.0243 1200 -0.1471  0.7455
## 361  Occupancy                  Gray Catbird      dicot  0.2751 0.1854 -0.0950  0.2768  0.6439 1.0016 1200 -0.0243  0.5850
## 362  Occupancy                   Green Heron      dicot  0.2441 0.2648 -0.2805  0.2499  0.7609 1.0012 1200 -0.1879  0.6658
## 363  Occupancy              Hairy Woodpecker      dicot  0.3135 0.2699 -0.2180  0.3069  0.8615 1.0134 1200 -0.1105  0.7667
## 364  Occupancy                  Herring Gull      dicot  0.2664 0.2699 -0.2714  0.2657  0.7981 1.0143 1200 -0.1682  0.7207
## 365  Occupancy                 Hermit Thrush      dicot  0.2767 0.2526 -0.2237  0.2670  0.7564 1.0006 1200 -0.1249  0.6881
## 366  Occupancy                   House Finch      dicot  0.0575 0.2517 -0.4521  0.0645  0.5242 1.0184 1200 -0.3506  0.4409
## 367  Occupancy                 House Sparrow      dicot  0.0181 0.2212 -0.4373  0.0309  0.4194 1.0122 1094 -0.3536  0.3393
## 368  Occupancy                Hooded Warbler      dicot  0.6466 0.2288  0.2441  0.6274  1.1206 1.0002 1090  0.3038  1.0331
## 369  Occupancy                    House Wren      dicot  0.0793 0.1771 -0.2895  0.0825  0.4042 1.0071 1200 -0.2164  0.3600
## 370  Occupancy                Indigo Bunting      dicot  0.3689 0.1909  0.0195  0.3568  0.7637 1.0093 1244  0.0631  0.6901
## 371  Occupancy                      Killdeer      dicot  0.2869 0.2397 -0.1967  0.2882  0.7670 1.0029 1200 -0.1081  0.6986
## 372  Occupancy         Louisiana Waterthrush      dicot  0.4024 0.2339 -0.0454  0.3914  0.8804 1.0040 1617  0.0262  0.7922
## 373  Occupancy                       Mallard      dicot  0.2246 0.2529 -0.2779  0.2219  0.7303 1.0239 1200 -0.2080  0.6344
## 374  Occupancy                 Mourning Dove      dicot  0.2739 0.2246 -0.1554  0.2715  0.7160 1.0125 1200 -0.0669  0.6387
## 375  Occupancy             Northern Cardinal      dicot  0.2114 0.2428 -0.2551  0.2232  0.6782 1.0009 1200 -0.1818  0.6018
## 376  Occupancy              Northern Flicker      dicot  0.2540 0.2434 -0.2208  0.2434  0.7494 1.0173 1200 -0.1412  0.6561
## 377  Occupancy               Northern Parula      dicot  0.1634 0.2718 -0.4042  0.1728  0.6955 1.0006 1097 -0.2943  0.5996
## 378  Occupancy Northern Rough-winged Swallow      dicot  0.3713 0.2457 -0.0937  0.3724  0.8698 1.0095 1200 -0.0284  0.7875
## 379  Occupancy                Orchard Oriole      dicot  0.1159 0.2379 -0.3783  0.1320  0.5383 1.0009 1200 -0.2816  0.4816
## 380  Occupancy                      Ovenbird      dicot  0.2432 0.2176 -0.1739  0.2396  0.6954 1.0028 1200 -0.1181  0.6090
## 381  Occupancy           Pileated Woodpecker      dicot  0.3275 0.2561 -0.1607  0.3262  0.8490 1.0006 1011 -0.0907  0.7487
## 382  Occupancy                  Purple Finch      dicot  0.2484 0.2588 -0.2777  0.2491  0.7439 1.0161 1200 -0.1670  0.6583
## 383  Occupancy                 Purple Martin      dicot  0.2436 0.2709 -0.2831  0.2406  0.7789 1.0050 1200 -0.2017  0.6728
## 384  Occupancy        Rose-breasted Grosbeak      dicot  0.1112 0.2407 -0.3742  0.1193  0.5656 1.0039 1320 -0.2780  0.4885
## 385  Occupancy              Ring-billed Gull      dicot  0.1265 0.2355 -0.3531  0.1313  0.5677 1.0030 1200 -0.2776  0.5051
## 386  Occupancy         Red-breasted Nuthatch      dicot  0.2550 0.2709 -0.3029  0.2596  0.7769 1.0008 1200 -0.1908  0.6978
## 387  Occupancy        Red-bellied Woodpecker      dicot  0.3814 0.2517 -0.1089  0.3733  0.8915 1.0016 1200 -0.0108  0.8186
## 388  Occupancy                Red-eyed Vireo      dicot  0.4146 0.2382 -0.0364  0.3984  0.9473 1.0071 1200  0.0418  0.8307
## 389  Occupancy         Red-headed Woodpecker      dicot  0.1609 0.2455 -0.3636  0.1642  0.6467 1.0002 1200 -0.2489  0.5478
## 390  Occupancy                   Rock Pigeon      dicot  0.1738 0.2546 -0.3491  0.1748  0.6600 1.0086 1200 -0.2640  0.5844
## 391  Occupancy           Red-shouldered Hawk      dicot  0.2361 0.2579 -0.2825  0.2376  0.7292 1.0090 1200 -0.1696  0.6597
## 392  Occupancy               Red-tailed Hawk      dicot -0.0576 0.2737 -0.6410 -0.0391  0.4579 1.0377 1054 -0.5247  0.3581
## 393  Occupancy     Ruby-throated Hummingbird      dicot  0.3554 0.2922 -0.2330  0.3514  0.9566 1.0029 1096 -0.1164  0.8619
## 394  Occupancy          Red-winged Blackbird      dicot  0.0752 0.1873 -0.2810  0.0729  0.4477 1.0007 1109 -0.2330  0.3908
## 395  Occupancy              Savannah Sparrow      dicot  0.2417 0.2622 -0.2784  0.2490  0.7534 1.0093 1496 -0.1935  0.6723
## 396  Occupancy               Scarlet Tanager      dicot  0.3015 0.2383 -0.1430  0.2930  0.7897 0.9996 1046 -0.0706  0.7087
## 397  Occupancy                  Song Sparrow      dicot  0.1866 0.1799 -0.1544  0.1864  0.5571 1.0170 1200 -0.1071  0.4762
## 398  Occupancy                 Swamp Sparrow      dicot  0.1547 0.2412 -0.3454  0.1649  0.6169 1.0031 1200 -0.2611  0.5352
## 399  Occupancy             Tennessee Warbler      dicot  0.2340 0.2691 -0.3087  0.2305  0.7452 0.9991 1200 -0.2001  0.6544
## 400  Occupancy                  Tree Swallow      dicot  0.2025 0.2450 -0.3065  0.2109  0.6683 1.0098 1200 -0.2011  0.5846
## 401  Occupancy               Tufted Titmouse      dicot  0.2844 0.2413 -0.1685  0.2788  0.7870 1.0068  973 -0.1099  0.6858
## 402  Occupancy                Turkey Vulture      dicot  0.2144 0.2556 -0.2740  0.2118  0.7192 1.0013 1200 -0.2055  0.6327
## 403  Occupancy                         Veery      dicot  0.3327 0.2254 -0.1005  0.3344  0.7945 1.0098 1078 -0.0340  0.6877
## 404  Occupancy                 Virginia Rail      dicot  0.2352 0.2733 -0.3214  0.2402  0.7897 1.0062 1200 -0.2367  0.6851
## 405  Occupancy                Warbling Vireo      dicot  0.3303 0.2058 -0.0548  0.3277  0.7301 1.0056 1200 -0.0003  0.6592
## 406  Occupancy       White-breasted Nuthatch      dicot  0.3405 0.2516 -0.1496  0.3307  0.8615 1.0008 1200 -0.0466  0.7766
## 407  Occupancy              White-eyed Vireo      dicot  0.3063 0.2593 -0.2061  0.3002  0.8267 1.0142 1200 -0.1204  0.7369
## 408  Occupancy             Willow Flycatcher      dicot  0.1644 0.2373 -0.3045  0.1726  0.6091 1.0033 1322 -0.2248  0.5402
## 409  Occupancy                   Wild Turkey      dicot  0.1945 0.2607 -0.3094  0.1972  0.7378 0.9999  889 -0.2352  0.6221
## 410  Occupancy                   Winter Wren      dicot  0.2290 0.2463 -0.2534  0.2360  0.7076 1.0005 1200 -0.1868  0.6240
## 411  Occupancy                     Wood Duck      dicot  0.2643 0.2576 -0.2570  0.2511  0.7788 0.9996 1200 -0.1540  0.7002
## 412  Occupancy                   Wood Thrush      dicot  0.3277 0.2178 -0.0890  0.3224  0.7861 1.0043 1043 -0.0274  0.6983
## 413  Occupancy          Yellow-billed Cuckoo      dicot  0.2763 0.2595 -0.2121  0.2756  0.8054 1.0044 1200 -0.1558  0.6948
## 414  Occupancy                Yellow Warbler      dicot  0.1805 0.1974 -0.2029  0.1825  0.5771 1.0021  927 -0.1286  0.5142
## 415  Occupancy         Yellow-throated Vireo      dicot  0.2242 0.2465 -0.2795  0.2261  0.7290 1.0050 1200 -0.1749  0.6239
## 416  Occupancy       Yellow-throated Warbler      dicot  0.4259 0.2529 -0.0371  0.4117  0.9493 1.0158 1200  0.0333  0.8681
## 417  Occupancy            Acadian Flycatcher      cyper  0.0725 0.1911 -0.2847  0.0692  0.4625 1.0010 1589 -0.2265  0.4039
## 418  Occupancy              Alder Flycatcher      cyper  0.0391 0.3139 -0.5553  0.0254  0.6566 1.0056 1568 -0.4649  0.5607
## 419  Occupancy                 American Crow      cyper  0.0920 0.2100 -0.3169  0.0935  0.5155 1.0017 1445 -0.2502  0.4414
## 420  Occupancy            American Goldfinch      cyper  0.0504 0.2661 -0.4653  0.0593  0.5874 1.0038 1200 -0.3943  0.5037
## 421  Occupancy              American Kestrel      cyper -0.2569 0.3175 -0.8825 -0.2503  0.3589 1.0007 1200 -0.7991  0.2443
## 422  Occupancy             American Redstart      cyper -0.1111 0.2579 -0.6041 -0.1196  0.4137 1.0058 1200 -0.5302  0.3149
## 423  Occupancy                American Robin      cyper  0.0630 0.2319 -0.3574  0.0539  0.5376 1.0014 1200 -0.2965  0.4637
## 424  Occupancy             American Woodcock      cyper -0.0741 0.3115 -0.6894 -0.0711  0.5197 1.0063 1200 -0.5968  0.4309
## 425  Occupancy                    Barred Owl      cyper -0.2580 0.3116 -0.9114 -0.2344  0.3032 1.0013 1200 -0.7863  0.2265
## 426  Occupancy                    Bald Eagle      cyper -0.3192 0.3249 -0.9762 -0.3163  0.3230 1.0093 1200 -0.8630  0.2041
## 427  Occupancy                  Bank Swallow      cyper -0.2781 0.3166 -0.9481 -0.2690  0.2937 1.0007 1148 -0.8163  0.2138
## 428  Occupancy              Baltimore Oriole      cyper -0.4183 0.2275 -0.8687 -0.4113  0.0114 1.0003 1200 -0.7972 -0.0603
## 429  Occupancy                  Barn Swallow      cyper -0.3091 0.2758 -0.8687 -0.3032  0.2197 1.0053 1200 -0.7684  0.1390
## 430  Occupancy        Black-capped Chickadee      cyper  0.0192 0.2810 -0.5120  0.0201  0.5853 1.0083 1200 -0.4377  0.4817
## 431  Occupancy             Belted Kingfisher      cyper -0.5290 0.2800 -1.0851 -0.5156  0.0041 0.9990 1337 -0.9962 -0.0810
## 432  Occupancy         Blue-gray Gnatcatcher      cyper -0.0160 0.2323 -0.4340 -0.0250  0.4588 1.0117 1200 -0.3721  0.3863
## 433  Occupancy          Brown-headed Cowbird      cyper -0.2099 0.2466 -0.6930 -0.2079  0.3032 1.0050 1319 -0.6107  0.1867
## 434  Occupancy             Blue-headed Vireo      cyper -0.0633 0.3238 -0.6578 -0.0636  0.5937 0.9990 1200 -0.5830  0.4406
## 435  Occupancy                      Blue Jay      cyper -0.0138 0.2394 -0.4714 -0.0164  0.4630 1.0202 1200 -0.3989  0.3955
## 436  Occupancy                      Bobolink      cyper -0.1328 0.3232 -0.7372 -0.1512  0.5118 0.9999 1914 -0.6664  0.4006
## 437  Occupancy                 Brown Creeper      cyper  0.0615 0.2584 -0.4285  0.0580  0.5484 1.0347 1084 -0.3544  0.4777
## 438  Occupancy                Brown Thrasher      cyper -0.1177 0.3111 -0.7561 -0.1272  0.4862 0.9996 1200 -0.6322  0.4012
## 439  Occupancy  Black-throated Green Warbler      cyper -0.1274 0.3316 -0.7708 -0.1257  0.4907 1.0038 1200 -0.6559  0.4035
## 440  Occupancy             Broad-winged Hawk      cyper -0.2604 0.3182 -0.8923 -0.2551  0.3640 1.0053 1200 -0.8049  0.2734
## 441  Occupancy           Blue-winged Warbler      cyper  0.1264 0.2716 -0.3862  0.1269  0.6738 1.0007 1200 -0.3181  0.5723
## 442  Occupancy                  Canada Goose      cyper -0.0649 0.2845 -0.6386 -0.0599  0.4710 1.0023 1200 -0.5265  0.4044
## 443  Occupancy                 Carolina Wren      cyper -0.2499 0.2141 -0.6623 -0.2483  0.1410 1.0042 1200 -0.5949  0.0886
## 444  Occupancy                 Cedar Waxwing      cyper -0.1322 0.2140 -0.5312 -0.1359  0.3037 0.9999 1200 -0.4692  0.2177
## 445  Occupancy              Cerulean Warbler      cyper -0.1204 0.3255 -0.7451 -0.1218  0.5539 1.0045 1200 -0.6576  0.4068
## 446  Occupancy              Chipping Sparrow      cyper -0.0071 0.2263 -0.4320 -0.0054  0.4430 1.0114 1348 -0.3666  0.3649
## 447  Occupancy                 Chimney Swift      cyper -0.3027 0.2608 -0.8237 -0.3032  0.2051 1.0104 1200 -0.7298  0.1184
## 448  Occupancy                 Cliff Swallow      cyper -0.2559 0.3232 -0.8809 -0.2626  0.3553 1.0138 1200 -0.7893  0.2868
## 449  Occupancy                Common Grackle      cyper -0.1743 0.2241 -0.6211 -0.1701  0.2780 1.0016 1519 -0.5573  0.1805
## 450  Occupancy                 Cooper's Hawk      cyper -0.2089 0.2663 -0.7545 -0.1989  0.2727 1.0025 1200 -0.6647  0.2149
## 451  Occupancy           Common Yellowthroat      cyper  0.1954 0.1981 -0.1735  0.1912  0.6064 0.9995 1200 -0.1091  0.5289
## 452  Occupancy               Dark-eyed Junco      cyper -0.3371 0.2489 -0.8385 -0.3321  0.1395 1.0046 1200 -0.7572  0.0516
## 453  Occupancy              Downy Woodpecker      cyper  0.0187 0.2690 -0.4866  0.0174  0.5735 1.0044 1200 -0.3985  0.4781
## 454  Occupancy              Eastern Bluebird      cyper  0.2823 0.2375 -0.1714  0.2747  0.7750 1.0086 1098 -0.1005  0.7019
## 455  Occupancy              Eastern Kingbird      cyper -0.1865 0.2666 -0.7298 -0.1802  0.3191 1.0262 1101 -0.6298  0.2465
## 456  Occupancy            Eastern Meadowlark      cyper -0.2418 0.3135 -0.8947 -0.2472  0.3746 0.9998 1046 -0.7507  0.2779
## 457  Occupancy                Eastern Phoebe      cyper -0.2895 0.2494 -0.8076 -0.2851  0.2035 1.0018 1200 -0.6960  0.1163
## 458  Occupancy                Eastern Towhee      cyper  0.5798 0.2334  0.1242  0.5781  1.0428 1.0097 1200  0.2069  0.9593
## 459  Occupancy            Eastern Wood-Pewee      cyper -0.1182 0.2443 -0.5750 -0.1134  0.3532 1.0217 1200 -0.5190  0.2795
## 460  Occupancy             European Starling      cyper -0.4398 0.2587 -0.9676 -0.4314  0.0273 1.0020 1200 -0.8863 -0.0413
## 461  Occupancy                 Field Sparrow      cyper  0.2881 0.2548 -0.2031  0.2862  0.7816 0.9995 1200 -0.1203  0.7096
## 462  Occupancy              Great Blue Heron      cyper -0.5325 0.3044 -1.1551 -0.5271  0.0396 1.0020 1200 -1.0545 -0.0694
## 463  Occupancy      Great Crested Flycatcher      cyper -0.1717 0.2827 -0.7247 -0.1798  0.3872 0.9997 1200 -0.6219  0.2968
## 464  Occupancy              Great Horned Owl      cyper -0.2324 0.3241 -0.8965 -0.2291  0.3598 1.0098 1010 -0.7836  0.2791
## 465  Occupancy                  Gray Catbird      cyper -0.2294 0.1756 -0.5872 -0.2255  0.0942 1.0013 1200 -0.5281  0.0410
## 466  Occupancy                   Green Heron      cyper -0.0803 0.3151 -0.7039 -0.0765  0.5211 1.0039 1200 -0.6145  0.4422
## 467  Occupancy              Hairy Woodpecker      cyper  0.0743 0.2584 -0.4242  0.0764  0.5839 1.0029 1200 -0.3516  0.5098
## 468  Occupancy                  Herring Gull      cyper -0.2210 0.3160 -0.8473 -0.2201  0.3687 0.9998 1073 -0.7427  0.2829
## 469  Occupancy                 Hermit Thrush      cyper -0.0026 0.2993 -0.5975 -0.0099  0.6151 1.0131 1200 -0.4785  0.4956
## 470  Occupancy                   House Finch      cyper -0.2726 0.2740 -0.8314 -0.2683  0.2844 1.0114 1200 -0.7277  0.1764
## 471  Occupancy                 House Sparrow      cyper -0.3832 0.2259 -0.8671 -0.3730  0.0238 1.0022 1200 -0.7696 -0.0229
## 472  Occupancy                Hooded Warbler      cyper  0.0630 0.1921 -0.3181  0.0640  0.4521 1.0039 1050 -0.2590  0.3735
## 473  Occupancy                    House Wren      cyper  0.1942 0.1764 -0.1389  0.1939  0.5229 1.0089 1200 -0.0884  0.4813
## 474  Occupancy                Indigo Bunting      cyper -0.3498 0.1796 -0.6991 -0.3429 -0.0115 1.0020 1200 -0.6509 -0.0592
## 475  Occupancy                      Killdeer      cyper -0.0971 0.2864 -0.6423 -0.1007  0.4906 1.0012 1200 -0.5594  0.3776
## 476  Occupancy         Louisiana Waterthrush      cyper -0.3462 0.2561 -0.8355 -0.3443  0.1215 1.0009 1200 -0.7666  0.0581
## 477  Occupancy                       Mallard      cyper -0.2313 0.2946 -0.8409 -0.2182  0.3442 1.0092 1200 -0.7271  0.2385
## 478  Occupancy                 Mourning Dove      cyper  0.1008 0.2332 -0.3410  0.0927  0.5757 1.0007 1200 -0.2698  0.4957
## 479  Occupancy             Northern Cardinal      cyper -0.2480 0.2402 -0.7233 -0.2485  0.2366 1.0034 1200 -0.6273  0.1546
## 480  Occupancy              Northern Flicker      cyper  0.1770 0.3013 -0.4349  0.1888  0.7543 1.0234 1055 -0.3200  0.6439
## 481  Occupancy               Northern Parula      cyper -0.2315 0.3174 -0.8537 -0.2307  0.3677 1.0036 1456 -0.7416  0.2846
## 482  Occupancy Northern Rough-winged Swallow      cyper -0.4750 0.2906 -1.0461 -0.4692  0.0887 1.0086 1200 -0.9405 -0.0125
## 483  Occupancy                Orchard Oriole      cyper -0.2438 0.2708 -0.7979 -0.2403  0.2441 0.9995 1509 -0.7066  0.1895
## 484  Occupancy                      Ovenbird      cyper -0.2147 0.2487 -0.7412 -0.2092  0.2627 1.0053 1200 -0.6273  0.1896
## 485  Occupancy           Pileated Woodpecker      cyper -0.0928 0.2764 -0.6614 -0.0937  0.4410 1.0045 1200 -0.5302  0.3357
## 486  Occupancy                  Purple Finch      cyper -0.1798 0.3249 -0.8311 -0.1699  0.4532 1.0033 1200 -0.6973  0.3290
## 487  Occupancy                 Purple Martin      cyper -0.1511 0.3450 -0.8643 -0.1366  0.5395 1.0173 1200 -0.7112  0.4090
## 488  Occupancy        Rose-breasted Grosbeak      cyper -0.2590 0.2654 -0.8044 -0.2576  0.2623 1.0024 1925 -0.6891  0.1733
## 489  Occupancy              Ring-billed Gull      cyper -0.3772 0.2728 -0.9232 -0.3797  0.1387 1.0042 1200 -0.8363  0.0521
## 490  Occupancy         Red-breasted Nuthatch      cyper -0.0447 0.3226 -0.6935 -0.0510  0.6024 0.9994 1633 -0.5768  0.4652
## 491  Occupancy        Red-bellied Woodpecker      cyper -0.1821 0.3103 -0.7868 -0.1908  0.4098 0.9996 1200 -0.6772  0.3204
## 492  Occupancy                Red-eyed Vireo      cyper -0.1068 0.2453 -0.6005 -0.1115  0.3909 1.0091 1200 -0.5139  0.3052
## 493  Occupancy         Red-headed Woodpecker      cyper -0.2308 0.2954 -0.8036 -0.2370  0.3519 1.0009 1200 -0.7171  0.2598
## 494  Occupancy                   Rock Pigeon      cyper -0.2372 0.3111 -0.8490 -0.2432  0.4073 1.0100 1200 -0.7374  0.2614
## 495  Occupancy           Red-shouldered Hawk      cyper -0.0682 0.2998 -0.6615 -0.0746  0.5346 1.0033 1200 -0.5455  0.4432
## 496  Occupancy               Red-tailed Hawk      cyper -0.3342 0.2905 -0.9290 -0.3288  0.2052 1.0139  799 -0.8422  0.1298
## 497  Occupancy     Ruby-throated Hummingbird      cyper -0.0275 0.3056 -0.6305 -0.0252  0.5685 1.0042 1200 -0.5212  0.4622
## 498  Occupancy          Red-winged Blackbird      cyper -0.2405 0.1888 -0.6353 -0.2413  0.1223 1.0027 1674 -0.5515  0.0788
## 499  Occupancy              Savannah Sparrow      cyper -0.2466 0.3181 -0.8845 -0.2370  0.3541 1.0133 1200 -0.7655  0.2814
## 500  Occupancy               Scarlet Tanager      cyper -0.1664 0.2283 -0.6124 -0.1643  0.2727 1.0021 1335 -0.5379  0.1995
## 501  Occupancy                  Song Sparrow      cyper -0.0098 0.1692 -0.3366 -0.0126  0.3336 0.9999 1009 -0.2786  0.2768
## 502  Occupancy                 Swamp Sparrow      cyper -0.1190 0.2623 -0.6302 -0.1194  0.3926 1.0077 1200 -0.5514  0.3274
## 503  Occupancy             Tennessee Warbler      cyper -0.1441 0.3288 -0.8379 -0.1366  0.4662 1.0044 1350 -0.7092  0.3770
## 504  Occupancy                  Tree Swallow      cyper -0.3167 0.2720 -0.8716 -0.3011  0.1920 1.0028 1200 -0.7831  0.0999
## 505  Occupancy               Tufted Titmouse      cyper -0.1585 0.2592 -0.6686 -0.1602  0.3625 1.0176 1200 -0.5944  0.2617
## 506  Occupancy                Turkey Vulture      cyper -0.0741 0.2894 -0.6484 -0.0769  0.5226 1.0024 1200 -0.5618  0.3955
## 507  Occupancy                         Veery      cyper -0.0749 0.2509 -0.5282 -0.0781  0.4160 1.0181 1200 -0.4750  0.3514
## 508  Occupancy                 Virginia Rail      cyper -0.1419 0.3314 -0.8114 -0.1359  0.4820 1.0101 1200 -0.7109  0.4097
## 509  Occupancy                Warbling Vireo      cyper -0.4887 0.2333 -0.9620 -0.4797 -0.0570 1.0121 1200 -0.8889 -0.1189
## 510  Occupancy       White-breasted Nuthatch      cyper  0.0841 0.2765 -0.4788  0.0840  0.6189 1.0034 1391 -0.3671  0.5521
## 511  Occupancy              White-eyed Vireo      cyper -0.0861 0.3157 -0.7106 -0.0892  0.5433 1.0052 1200 -0.6083  0.4185
## 512  Occupancy             Willow Flycatcher      cyper  0.0617 0.2563 -0.4161  0.0518  0.6057 1.0041 1200 -0.3436  0.5061
## 513  Occupancy                   Wild Turkey      cyper  0.0628 0.3075 -0.5420  0.0575  0.6566 1.0241 1200 -0.4413  0.5600
## 514  Occupancy                   Winter Wren      cyper -0.0734 0.2988 -0.6602 -0.0688  0.4997 1.0104 1200 -0.5685  0.4216
## 515  Occupancy                     Wood Duck      cyper -0.1894 0.3100 -0.7971 -0.1898  0.4201 1.0211 1200 -0.7055  0.3002
## 516  Occupancy                   Wood Thrush      cyper -0.0567 0.2129 -0.4907 -0.0554  0.3534 1.0056 1200 -0.4100  0.2928
## 517  Occupancy          Yellow-billed Cuckoo      cyper -0.2149 0.2940 -0.8167 -0.2058  0.3603 0.9992 1445 -0.7093  0.2693
## 518  Occupancy                Yellow Warbler      cyper -0.2215 0.2106 -0.6288 -0.2251  0.2111 1.0043 1200 -0.5641  0.1335
## 519  Occupancy         Yellow-throated Vireo      cyper -0.0746 0.2536 -0.5604 -0.0713  0.4456 1.0082 1200 -0.4823  0.3456
## 520  Occupancy       Yellow-throated Warbler      cyper -0.4352 0.3031 -1.1007 -0.4104  0.0895 1.0031 1038 -0.9822  0.0162
## 521  Occupancy            Acadian Flycatcher small_tree  0.0561 0.1394 -0.2094  0.0518  0.3223 1.0018 1200 -0.1616  0.2857
## 522  Occupancy              Alder Flycatcher small_tree  0.1456 0.1839 -0.1945  0.1413  0.5432 1.0020 1200 -0.1497  0.4573
## 523  Occupancy                 American Crow small_tree  0.1072 0.1498 -0.1750  0.1059  0.3916 1.0004 1200 -0.1336  0.3527
## 524  Occupancy            American Goldfinch small_tree -0.0198 0.1704 -0.3537 -0.0125  0.3070 1.0172 1200 -0.3009  0.2519
## 525  Occupancy              American Kestrel small_tree  0.0688 0.1871 -0.2853  0.0723  0.4264 1.0016  997 -0.2314  0.3784
## 526  Occupancy             American Redstart small_tree  0.0338 0.1650 -0.3027  0.0371  0.3461 1.0042 1217 -0.2465  0.3026
## 527  Occupancy                American Robin small_tree  0.0999 0.1579 -0.2227  0.0994  0.4170 1.0134 1200 -0.1518  0.3598
## 528  Occupancy             American Woodcock small_tree  0.1532 0.1793 -0.1652  0.1402  0.5364 0.9994 1069 -0.1264  0.4627
## 529  Occupancy                    Barred Owl small_tree  0.0666 0.1772 -0.2672  0.0665  0.4150 1.0022 1200 -0.2222  0.3589
## 530  Occupancy                    Bald Eagle small_tree  0.1163 0.1724 -0.2244  0.1153  0.4691 1.0223 1200 -0.1618  0.3977
## 531  Occupancy                  Bank Swallow small_tree  0.0665 0.1845 -0.3047  0.0664  0.4233 1.0035 1797 -0.2384  0.3617
## 532  Occupancy              Baltimore Oriole small_tree  0.0948 0.1587 -0.2166  0.0915  0.3941 1.0054 1123 -0.1702  0.3523
## 533  Occupancy                  Barn Swallow small_tree  0.0785 0.1617 -0.2274  0.0767  0.4045 1.0078 1200 -0.1844  0.3477
## 534  Occupancy        Black-capped Chickadee small_tree  0.0569 0.1773 -0.2864  0.0531  0.4199 1.0107 1200 -0.2278  0.3601
## 535  Occupancy             Belted Kingfisher small_tree  0.0129 0.1684 -0.3320  0.0195  0.3176 0.9994 1200 -0.2704  0.2739
## 536  Occupancy         Blue-gray Gnatcatcher small_tree  0.1156 0.1594 -0.1857  0.1142  0.4185 1.0051 1200 -0.1353  0.3779
## 537  Occupancy          Brown-headed Cowbird small_tree  0.1114 0.1703 -0.2420  0.1098  0.4617 1.0077 1200 -0.1605  0.4094
## 538  Occupancy             Blue-headed Vireo small_tree  0.0623 0.1828 -0.2904  0.0683  0.4357 1.0026 1200 -0.2326  0.3502
## 539  Occupancy                      Blue Jay small_tree  0.2300 0.1661 -0.0775  0.2211  0.5794 1.0042 1200 -0.0335  0.5163
## 540  Occupancy                      Bobolink small_tree  0.0677 0.1812 -0.2951  0.0704  0.4177 1.0171 1200 -0.2211  0.3617
## 541  Occupancy                 Brown Creeper small_tree  0.0975 0.1650 -0.2158  0.0950  0.4128 1.0085 1200 -0.1778  0.3694
## 542  Occupancy                Brown Thrasher small_tree -0.0497 0.1879 -0.4405 -0.0468  0.3180 1.0036 1120 -0.3536  0.2452
## 543  Occupancy  Black-throated Green Warbler small_tree  0.0599 0.1913 -0.3213  0.0663  0.4243 1.0107 1200 -0.2582  0.3652
## 544  Occupancy             Broad-winged Hawk small_tree -0.0009 0.1857 -0.3813  0.0026  0.3494 1.0013 1200 -0.3038  0.2951
## 545  Occupancy           Blue-winged Warbler small_tree  0.0841 0.1681 -0.2387  0.0841  0.4274 1.0007 1200 -0.1943  0.3698
## 546  Occupancy                  Canada Goose small_tree  0.0434 0.1808 -0.3414  0.0476  0.3941 1.0058 1343 -0.2697  0.3255
## 547  Occupancy                 Carolina Wren small_tree  0.2203 0.1626 -0.0993  0.2193  0.5302 1.0014 1200 -0.0493  0.4786
## 548  Occupancy                 Cedar Waxwing small_tree -0.0836 0.1589 -0.4192 -0.0800  0.2169 1.0011 1200 -0.3410  0.1654
## 549  Occupancy              Cerulean Warbler small_tree  0.0612 0.1839 -0.2956  0.0627  0.4298 0.9994 1574 -0.2357  0.3674
## 550  Occupancy              Chipping Sparrow small_tree  0.0807 0.1551 -0.2214  0.0802  0.3986 0.9999 1026 -0.1663  0.3531
## 551  Occupancy                 Chimney Swift small_tree -0.0477 0.1862 -0.3959 -0.0447  0.3084 1.0107 1200 -0.3510  0.2496
## 552  Occupancy                 Cliff Swallow small_tree  0.0150 0.1809 -0.3422  0.0136  0.3688 1.0153 1200 -0.2778  0.3159
## 553  Occupancy                Common Grackle small_tree  0.1013 0.1614 -0.1990  0.0954  0.4574 1.0013 1299 -0.1500  0.3914
## 554  Occupancy                 Cooper's Hawk small_tree  0.0634 0.1631 -0.2584  0.0691  0.3740 1.0009 1103 -0.2024  0.3200
## 555  Occupancy           Common Yellowthroat small_tree  0.0766 0.1414 -0.2121  0.0789  0.3531 1.0017 1200 -0.1574  0.3070
## 556  Occupancy               Dark-eyed Junco small_tree  0.0544 0.1642 -0.2713  0.0567  0.3820 1.0082 1103 -0.2281  0.3139
## 557  Occupancy              Downy Woodpecker small_tree -0.0013 0.1748 -0.3591  0.0025  0.3247 1.0094 1200 -0.3010  0.2862
## 558  Occupancy              Eastern Bluebird small_tree  0.0682 0.1621 -0.2302  0.0627  0.3893 1.0020 1200 -0.1870  0.3428
## 559  Occupancy              Eastern Kingbird small_tree  0.1243 0.1612 -0.1729  0.1230  0.4414 1.0075 1020 -0.1292  0.3910
## 560  Occupancy            Eastern Meadowlark small_tree  0.0729 0.1810 -0.2805  0.0761  0.4243 1.0000 1312 -0.2260  0.3637
## 561  Occupancy                Eastern Phoebe small_tree  0.0148 0.1655 -0.3214  0.0191  0.3162 1.0105 1200 -0.2595  0.2836
## 562  Occupancy                Eastern Towhee small_tree  0.1235 0.1478 -0.1578  0.1205  0.4224 1.0029 1200 -0.1076  0.3808
## 563  Occupancy            Eastern Wood-Pewee small_tree  0.1624 0.1545 -0.1360  0.1549  0.4835 1.0048 1200 -0.0886  0.4383
## 564  Occupancy             European Starling small_tree -0.0546 0.1528 -0.3849 -0.0507  0.2353 1.0089 1200 -0.3167  0.1873
## 565  Occupancy                 Field Sparrow small_tree  0.0273 0.1538 -0.2645  0.0274  0.3153 1.0218 1200 -0.2190  0.2775
## 566  Occupancy              Great Blue Heron small_tree  0.0688 0.1707 -0.2678  0.0673  0.4070 0.9996 1200 -0.2278  0.3361
## 567  Occupancy      Great Crested Flycatcher small_tree  0.0365 0.1888 -0.3436  0.0351  0.4136 1.0014 1123 -0.2739  0.3557
## 568  Occupancy              Great Horned Owl small_tree  0.0550 0.1850 -0.3281  0.0587  0.3996 1.0030 1078 -0.2531  0.3479
## 569  Occupancy                  Gray Catbird small_tree  0.0865 0.1410 -0.1837  0.0883  0.3545 1.0030 1200 -0.1466  0.3186
## 570  Occupancy                   Green Heron small_tree  0.0928 0.1796 -0.2562  0.0881  0.4465 1.0120 1200 -0.1948  0.3971
## 571  Occupancy              Hairy Woodpecker small_tree  0.1825 0.1704 -0.1387  0.1827  0.5354 1.0065 1200 -0.0935  0.4621
## 572  Occupancy                  Herring Gull small_tree  0.0797 0.1846 -0.2661  0.0738  0.4471 1.0053 1074 -0.2143  0.3912
## 573  Occupancy                 Hermit Thrush small_tree  0.0674 0.1821 -0.2754  0.0637  0.4360 1.0019 1322 -0.2112  0.3652
## 574  Occupancy                   House Finch small_tree  0.1161 0.1684 -0.2088  0.1170  0.4544 1.0099 1320 -0.1714  0.3918
## 575  Occupancy                 House Sparrow small_tree  0.0683 0.1474 -0.2322  0.0732  0.3557 1.0041 1200 -0.1710  0.3085
## 576  Occupancy                Hooded Warbler small_tree -0.0012 0.1475 -0.3020  0.0025  0.2803 1.0065 1200 -0.2456  0.2374
## 577  Occupancy                    House Wren small_tree  0.2251 0.1377 -0.0286  0.2202  0.5133 1.0040 1200  0.0035  0.4540
## 578  Occupancy                Indigo Bunting small_tree  0.0562 0.1369 -0.2224  0.0617  0.3324 1.0035 1094 -0.1794  0.2779
## 579  Occupancy                      Killdeer small_tree  0.1041 0.1704 -0.2410  0.1074  0.4264 1.0091 1080 -0.1911  0.3801
## 580  Occupancy         Louisiana Waterthrush small_tree  0.1155 0.1618 -0.1868  0.1127  0.4509 1.0005 1200 -0.1469  0.3837
## 581  Occupancy                       Mallard small_tree  0.0371 0.1721 -0.2923  0.0356  0.3858 1.0098 1344 -0.2460  0.3201
## 582  Occupancy                 Mourning Dove small_tree  0.1283 0.1566 -0.1722  0.1211  0.4519 1.0032 1200 -0.1070  0.4066
## 583  Occupancy             Northern Cardinal small_tree  0.0392 0.1649 -0.2785  0.0458  0.3621 0.9992 1093 -0.2356  0.3053
## 584  Occupancy              Northern Flicker small_tree  0.0611 0.1830 -0.2802  0.0591  0.4406 1.0000 1200 -0.2398  0.3695
## 585  Occupancy               Northern Parula small_tree  0.0669 0.1813 -0.2843  0.0692  0.4141 1.0034  963 -0.2240  0.3620
## 586  Occupancy Northern Rough-winged Swallow small_tree  0.0076 0.1728 -0.3158  0.0073  0.3415 1.0010 1200 -0.2690  0.2848
## 587  Occupancy                Orchard Oriole small_tree  0.0201 0.1638 -0.3026  0.0228  0.3397 1.0082 1200 -0.2542  0.2806
## 588  Occupancy                      Ovenbird small_tree  0.0336 0.1645 -0.2897  0.0327  0.3500 1.0001 1200 -0.2392  0.3002
## 589  Occupancy           Pileated Woodpecker small_tree  0.0773 0.1715 -0.2485  0.0703  0.4283 1.0006 1200 -0.1915  0.3626
## 590  Occupancy                  Purple Finch small_tree  0.0434 0.1783 -0.3210  0.0393  0.3876 1.0059 1200 -0.2542  0.3376
## 591  Occupancy                 Purple Martin small_tree  0.0647 0.1858 -0.3023  0.0687  0.4267 1.0021 1200 -0.2378  0.3768
## 592  Occupancy        Rose-breasted Grosbeak small_tree -0.0348 0.1738 -0.3828 -0.0320  0.2827 1.0041 1200 -0.3230  0.2314
## 593  Occupancy              Ring-billed Gull small_tree  0.0523 0.1725 -0.2839  0.0499  0.3866 1.0018 1200 -0.2259  0.3299
## 594  Occupancy         Red-breasted Nuthatch small_tree  0.0580 0.1889 -0.3168  0.0559  0.4429 1.0013 1200 -0.2543  0.3615
## 595  Occupancy        Red-bellied Woodpecker small_tree  0.0336 0.1701 -0.2935  0.0312  0.3883 1.0019 1065 -0.2356  0.3223
## 596  Occupancy                Red-eyed Vireo small_tree -0.0729 0.1554 -0.3974 -0.0625  0.2097 1.0104 1200 -0.3378  0.1666
## 597  Occupancy         Red-headed Woodpecker small_tree  0.0521 0.1757 -0.3131  0.0532  0.3796 1.0007 1200 -0.2291  0.3372
## 598  Occupancy                   Rock Pigeon small_tree  0.0410 0.1864 -0.3486  0.0417  0.3965 0.9997 1200 -0.2731  0.3363
## 599  Occupancy           Red-shouldered Hawk small_tree  0.1732 0.1892 -0.1887  0.1750  0.5474 1.0022 1200 -0.1406  0.4765
## 600  Occupancy               Red-tailed Hawk small_tree  0.1236 0.1705 -0.1974  0.1230  0.4766 1.0041 1200 -0.1347  0.4169
## 601  Occupancy     Ruby-throated Hummingbird small_tree  0.0484 0.1913 -0.3385  0.0513  0.4134 1.0030 1376 -0.2826  0.3517
## 602  Occupancy          Red-winged Blackbird small_tree  0.0959 0.1368 -0.1714  0.0978  0.3678 1.0020 1200 -0.1294  0.3271
## 603  Occupancy              Savannah Sparrow small_tree  0.0689 0.1792 -0.2848  0.0639  0.4352 1.0036 1200 -0.2127  0.3594
## 604  Occupancy               Scarlet Tanager small_tree  0.0689 0.1505 -0.2330  0.0692  0.3542 1.0031 1304 -0.1838  0.3063
## 605  Occupancy                  Song Sparrow small_tree  0.0969 0.1341 -0.1566  0.0958  0.3699 0.9990 1200 -0.1169  0.3222
## 606  Occupancy                 Swamp Sparrow small_tree  0.0518 0.1686 -0.2997  0.0570  0.3694 1.0014 1085 -0.2283  0.3201
## 607  Occupancy             Tennessee Warbler small_tree  0.0703 0.1865 -0.3022  0.0705  0.4433 1.0078 1200 -0.2378  0.3740
## 608  Occupancy                  Tree Swallow small_tree  0.0439 0.1567 -0.2745  0.0445  0.3466 1.0042 1200 -0.2169  0.2912
## 609  Occupancy               Tufted Titmouse small_tree  0.0959 0.1737 -0.2292  0.0929  0.4465 1.0013 1200 -0.1840  0.3866
## 610  Occupancy                Turkey Vulture small_tree  0.0430 0.1853 -0.3311  0.0436  0.4191 1.0014 1312 -0.2561  0.3458
## 611  Occupancy                         Veery small_tree  0.1061 0.1675 -0.2095  0.1010  0.4323 1.0023 1200 -0.1521  0.3810
## 612  Occupancy                 Virginia Rail small_tree  0.0631 0.1895 -0.3016  0.0678  0.4153 1.0040 1200 -0.2466  0.3738
## 613  Occupancy                Warbling Vireo small_tree  0.0038 0.1445 -0.2675  0.0016  0.2968 1.0051 1200 -0.2316  0.2489
## 614  Occupancy       White-breasted Nuthatch small_tree  0.1115 0.1656 -0.2065  0.1040  0.4576 1.0056 1347 -0.1512  0.3909
## 615  Occupancy              White-eyed Vireo small_tree  0.0692 0.1731 -0.2586  0.0668  0.4106 1.0076 1200 -0.2080  0.3555
## 616  Occupancy             Willow Flycatcher small_tree  0.0120 0.1615 -0.3178  0.0135  0.3212 1.0049 1337 -0.2572  0.2670
## 617  Occupancy                   Wild Turkey small_tree  0.0428 0.1790 -0.3021  0.0427  0.3956 0.9995 1200 -0.2502  0.3385
## 618  Occupancy                   Winter Wren small_tree  0.0114 0.1790 -0.3477  0.0131  0.3501 1.0235 1200 -0.2785  0.2993
## 619  Occupancy                     Wood Duck small_tree  0.0822 0.1833 -0.2763  0.0768  0.4474 1.0091 1200 -0.2168  0.3787
## 620  Occupancy                   Wood Thrush small_tree  0.0033 0.1439 -0.2853 -0.0003  0.2960 0.9995 1200 -0.2321  0.2406
## 621  Occupancy          Yellow-billed Cuckoo small_tree  0.0714 0.1732 -0.2841  0.0776  0.3821 1.0003 1200 -0.2048  0.3419
## 622  Occupancy                Yellow Warbler small_tree  0.0251 0.1444 -0.2452  0.0202  0.3211 1.0026 1200 -0.2114  0.2689
## 623  Occupancy         Yellow-throated Vireo small_tree  0.0189 0.1657 -0.3278  0.0244  0.3213 1.0015 1200 -0.2611  0.2788
## 624  Occupancy       Yellow-throated Warbler small_tree  0.2064 0.1837 -0.1323  0.1964  0.5848 1.0038 1200 -0.0700  0.5257
## 625  Occupancy            Acadian Flycatcher      shrub  0.2490 0.2048 -0.1385  0.2501  0.6738 1.0026 1200 -0.0846  0.6095
## 626  Occupancy              Alder Flycatcher      shrub -0.2691 0.2808 -0.8248 -0.2569  0.2436 1.0000 1200 -0.7341  0.1706
## 627  Occupancy                 American Crow      shrub -0.2427 0.1954 -0.6169 -0.2433  0.1389 1.0063 1200 -0.5518  0.0737
## 628  Occupancy            American Goldfinch      shrub -0.0547 0.2449 -0.5518 -0.0566  0.4406 0.9990 1200 -0.4604  0.3564
## 629  Occupancy              American Kestrel      shrub -0.2818 0.2843 -0.8634 -0.2696  0.2461 1.0101 1369 -0.7554  0.1721
## 630  Occupancy             American Redstart      shrub -0.1338 0.2303 -0.5997 -0.1437  0.3308 1.0012 1200 -0.5117  0.2482
## 631  Occupancy                American Robin      shrub -0.2455 0.2094 -0.6392 -0.2476  0.1682 1.0076 1082 -0.5893  0.1075
## 632  Occupancy             American Woodcock      shrub -0.1911 0.2645 -0.7456 -0.1915  0.3304 1.0033 1200 -0.6259  0.2391
## 633  Occupancy                    Barred Owl      shrub -0.1922 0.2700 -0.6874 -0.1907  0.3467 1.0021 1200 -0.6269  0.2706
## 634  Occupancy                    Bald Eagle      shrub -0.2919 0.2716 -0.8561 -0.2825  0.2235 1.0041 1200 -0.7305  0.1373
## 635  Occupancy                  Bank Swallow      shrub -0.2755 0.2804 -0.8833 -0.2587  0.2409 1.0051 1200 -0.7644  0.1884
## 636  Occupancy              Baltimore Oriole      shrub -0.1443 0.1947 -0.5044 -0.1441  0.2379 1.0083 1200 -0.4600  0.1656
## 637  Occupancy                  Barn Swallow      shrub -0.1975 0.2424 -0.6860 -0.1930  0.2835 1.0009 1200 -0.6102  0.1911
## 638  Occupancy        Black-capped Chickadee      shrub -0.0820 0.2503 -0.5351 -0.0904  0.4107 1.0024 1200 -0.4652  0.3191
## 639  Occupancy             Belted Kingfisher      shrub -0.1151 0.2351 -0.5706 -0.1215  0.3454 1.0008 1200 -0.5018  0.2666
## 640  Occupancy         Blue-gray Gnatcatcher      shrub -0.1635 0.2149 -0.5596 -0.1696  0.2867 1.0049 1200 -0.4908  0.2102
## 641  Occupancy          Brown-headed Cowbird      shrub -0.2145 0.2230 -0.6622 -0.2181  0.2235 1.0072 1362 -0.5870  0.1486
## 642  Occupancy             Blue-headed Vireo      shrub -0.1640 0.2812 -0.7057 -0.1682  0.4108 1.0017 1200 -0.6425  0.3098
## 643  Occupancy                      Blue Jay      shrub -0.0105 0.2243 -0.4217 -0.0234  0.4453 1.0008 1200 -0.3627  0.3531
## 644  Occupancy                      Bobolink      shrub -0.2186 0.2869 -0.7729 -0.2082  0.3342 0.9999 1200 -0.6927  0.2444
## 645  Occupancy                 Brown Creeper      shrub -0.1485 0.2338 -0.6218 -0.1493  0.3100 1.0019 1122 -0.5356  0.2298
## 646  Occupancy                Brown Thrasher      shrub -0.3302 0.2660 -0.8828 -0.3333  0.1941 1.0006 1200 -0.7686  0.1140
## 647  Occupancy  Black-throated Green Warbler      shrub -0.2224 0.2773 -0.7750 -0.2276  0.3086 1.0009 1200 -0.7022  0.2347
## 648  Occupancy             Broad-winged Hawk      shrub -0.2412 0.2598 -0.7540 -0.2410  0.2696 1.0036  909 -0.6564  0.1874
## 649  Occupancy           Blue-winged Warbler      shrub -0.1504 0.2460 -0.6269 -0.1561  0.3233 1.0004 1200 -0.5516  0.2494
## 650  Occupancy                  Canada Goose      shrub -0.2865 0.2549 -0.7985 -0.2767  0.1921 1.0100 1200 -0.7157  0.1150
## 651  Occupancy                 Carolina Wren      shrub -0.2538 0.2042 -0.6561 -0.2509  0.1411 1.0036 1200 -0.5940  0.0799
## 652  Occupancy                 Cedar Waxwing      shrub -0.6794 0.2214 -1.1477 -0.6637 -0.2850 1.0026 1200 -1.0672 -0.3508
## 653  Occupancy              Cerulean Warbler      shrub -0.2232 0.2812 -0.7940 -0.2311  0.3202 1.0034 1200 -0.6857  0.2602
## 654  Occupancy              Chipping Sparrow      shrub -0.1283 0.2093 -0.5216 -0.1326  0.2894 1.0048 1145 -0.4583  0.2230
## 655  Occupancy                 Chimney Swift      shrub -0.3930 0.2370 -0.8763 -0.3949  0.0734 1.0125 1200 -0.7838 -0.0106
## 656  Occupancy                 Cliff Swallow      shrub -0.2661 0.2893 -0.8437 -0.2724  0.3577 1.0087 1200 -0.7357  0.2036
## 657  Occupancy                Common Grackle      shrub -0.5561 0.2385 -1.0497 -0.5413 -0.1009 1.0045 1200 -0.9609 -0.1642
## 658  Occupancy                 Cooper's Hawk      shrub -0.2362 0.2413 -0.7308 -0.2390  0.2505 1.0037 1200 -0.6235  0.1668
## 659  Occupancy           Common Yellowthroat      shrub -0.4589 0.2064 -0.8574 -0.4614 -0.0612 1.0105 1200 -0.7869 -0.1206
## 660  Occupancy               Dark-eyed Junco      shrub -0.0566 0.2203 -0.4730 -0.0607  0.3750 1.0000 1200 -0.4031  0.3167
## 661  Occupancy              Downy Woodpecker      shrub -0.1819 0.2439 -0.6652 -0.1860  0.3009 1.0026 1200 -0.5743  0.1997
## 662  Occupancy              Eastern Bluebird      shrub -0.2717 0.2360 -0.7352 -0.2735  0.1869 1.0035 1200 -0.6490  0.1059
## 663  Occupancy              Eastern Kingbird      shrub -0.2447 0.2443 -0.7448 -0.2435  0.2140 1.0021 1200 -0.6621  0.1474
## 664  Occupancy            Eastern Meadowlark      shrub -0.2189 0.2725 -0.7608 -0.2165  0.3128 1.0037 1200 -0.6595  0.2266
## 665  Occupancy                Eastern Phoebe      shrub -0.2370 0.2193 -0.6662 -0.2371  0.1868 1.0275 1261 -0.6047  0.1008
## 666  Occupancy                Eastern Towhee      shrub -0.1761 0.1943 -0.5463 -0.1747  0.2061 1.0105 1578 -0.4884  0.1481
## 667  Occupancy            Eastern Wood-Pewee      shrub -0.1036 0.2143 -0.4926 -0.1104  0.3641 1.0007 1200 -0.4453  0.2542
## 668  Occupancy             European Starling      shrub -0.2960 0.2263 -0.7550 -0.2940  0.1298 1.0007 1200 -0.6815  0.0729
## 669  Occupancy                 Field Sparrow      shrub -0.4308 0.2544 -0.9790 -0.4154  0.0419 1.0180 1140 -0.8678 -0.0225
## 670  Occupancy              Great Blue Heron      shrub -0.0871 0.2547 -0.5712 -0.0920  0.4191 1.0021 1105 -0.4892  0.3420
## 671  Occupancy      Great Crested Flycatcher      shrub -0.1332 0.2472 -0.6015 -0.1345  0.3631 1.0005 1701 -0.5327  0.2768
## 672  Occupancy              Great Horned Owl      shrub -0.1768 0.2768 -0.6970 -0.1800  0.3664 1.0028 1200 -0.6218  0.2814
## 673  Occupancy                  Gray Catbird      shrub -0.2265 0.1796 -0.5725 -0.2259  0.1218 1.0046 1025 -0.5271  0.0557
## 674  Occupancy                   Green Heron      shrub -0.2719 0.2714 -0.8150 -0.2654  0.2826 1.0008 1200 -0.7101  0.1795
## 675  Occupancy              Hairy Woodpecker      shrub -0.3202 0.2575 -0.8336 -0.3162  0.2098 1.0094  973 -0.7253  0.1059
## 676  Occupancy                  Herring Gull      shrub -0.1722 0.2858 -0.7316 -0.1800  0.3771 1.0077 1200 -0.6482  0.2912
## 677  Occupancy                 Hermit Thrush      shrub -0.2269 0.2606 -0.7478 -0.2230  0.2583 1.0083 1200 -0.6621  0.1858
## 678  Occupancy                   House Finch      shrub  0.0222 0.2550 -0.4703  0.0217  0.5359 1.0018 1200 -0.3862  0.4467
## 679  Occupancy                 House Sparrow      shrub -0.0086 0.2086 -0.4005 -0.0084  0.4253 1.0140 1462 -0.3457  0.3421
## 680  Occupancy                Hooded Warbler      shrub  0.0486 0.1858 -0.2895  0.0498  0.4249 1.0011 1200 -0.2446  0.3631
## 681  Occupancy                    House Wren      shrub -0.3687 0.1729 -0.7130 -0.3650 -0.0339 1.0090 1200 -0.6552 -0.0821
## 682  Occupancy                Indigo Bunting      shrub -0.2629 0.1856 -0.6362 -0.2657  0.0976 1.0189 1149 -0.5732  0.0401
## 683  Occupancy                      Killdeer      shrub -0.1659 0.2440 -0.6380 -0.1635  0.3072 1.0056 1332 -0.5554  0.2356
## 684  Occupancy         Louisiana Waterthrush      shrub -0.2241 0.2265 -0.6728 -0.2239  0.2262 1.0000 1200 -0.6001  0.1465
## 685  Occupancy                       Mallard      shrub -0.2451 0.2550 -0.7500 -0.2372  0.2418 1.0032 1200 -0.6675  0.1681
## 686  Occupancy                 Mourning Dove      shrub -0.3231 0.2205 -0.7775 -0.3143  0.1150 1.0061 1200 -0.6916  0.0298
## 687  Occupancy             Northern Cardinal      shrub -0.2203 0.2192 -0.6491 -0.2171  0.1997 1.0090 1508 -0.5875  0.1458
## 688  Occupancy              Northern Flicker      shrub -0.2017 0.2580 -0.7378 -0.2053  0.2936 1.0065 1200 -0.6155  0.2130
## 689  Occupancy               Northern Parula      shrub -0.2826 0.2839 -0.8802 -0.2877  0.2450 1.0054 1200 -0.7643  0.1706
## 690  Occupancy Northern Rough-winged Swallow      shrub -0.3428 0.2489 -0.8466 -0.3381  0.1095 1.0023 1200 -0.7672  0.0455
## 691  Occupancy                Orchard Oriole      shrub -0.5201 0.2653 -1.1092 -0.5040 -0.0425 1.0037 1200 -0.9707 -0.1145
## 692  Occupancy                      Ovenbird      shrub -0.1124 0.2260 -0.5356 -0.1050  0.3248 1.0024 1200 -0.4757  0.2496
## 693  Occupancy           Pileated Woodpecker      shrub -0.2786 0.2601 -0.7897 -0.2718  0.2304 1.0276 1320 -0.7097  0.1326
## 694  Occupancy                  Purple Finch      shrub -0.2720 0.2779 -0.8717 -0.2656  0.2662 1.0166 1200 -0.7453  0.1679
## 695  Occupancy                 Purple Martin      shrub -0.2137 0.2859 -0.7774 -0.2123  0.3359 1.0059 1326 -0.6826  0.2728
## 696  Occupancy        Rose-breasted Grosbeak      shrub -0.3067 0.2197 -0.7206 -0.3152  0.0979 1.0138 1200 -0.6582  0.0527
## 697  Occupancy              Ring-billed Gull      shrub -0.2521 0.2361 -0.7416 -0.2452  0.2237 1.0036 1200 -0.6430  0.1206
## 698  Occupancy         Red-breasted Nuthatch      shrub -0.2734 0.2678 -0.8510 -0.2677  0.2489 1.0067 1406 -0.7188  0.1707
## 699  Occupancy        Red-bellied Woodpecker      shrub -0.2202 0.2375 -0.6542 -0.2255  0.2687 1.0072 1200 -0.5915  0.1734
## 700  Occupancy                Red-eyed Vireo      shrub -0.1207 0.2121 -0.5231 -0.1230  0.3149 1.0050 1200 -0.4514  0.2144
## 701  Occupancy         Red-headed Woodpecker      shrub -0.3168 0.2591 -0.8608 -0.3129  0.1594 1.0095 1200 -0.7565  0.0903
## 702  Occupancy                   Rock Pigeon      shrub -0.3207 0.2681 -0.8669 -0.3133  0.1785 1.0096 1200 -0.7666  0.0938
## 703  Occupancy           Red-shouldered Hawk      shrub -0.2987 0.2630 -0.8176 -0.3001  0.2285 1.0065 1200 -0.7165  0.1415
## 704  Occupancy               Red-tailed Hawk      shrub -0.2266 0.2611 -0.7476 -0.2250  0.2751 1.0151 1200 -0.6560  0.2012
## 705  Occupancy     Ruby-throated Hummingbird      shrub -0.2019 0.2447 -0.6866 -0.2063  0.2989 1.0071 1200 -0.5943  0.2111
## 706  Occupancy          Red-winged Blackbird      shrub -0.3239 0.1886 -0.7012 -0.3193  0.0274 1.0064 1200 -0.6465 -0.0209
## 707  Occupancy              Savannah Sparrow      shrub -0.2716 0.2793 -0.8264 -0.2663  0.2852 1.0150 1200 -0.7534  0.1726
## 708  Occupancy               Scarlet Tanager      shrub  0.1417 0.2167 -0.2347  0.1302  0.5738 1.0137 1312 -0.1809  0.5015
## 709  Occupancy                  Song Sparrow      shrub -0.3482 0.1784 -0.7286 -0.3477 -0.0024 1.0098 1200 -0.6450 -0.0550
## 710  Occupancy                 Swamp Sparrow      shrub -0.1685 0.2405 -0.6543 -0.1721  0.3035 1.0168 1200 -0.5622  0.2221
## 711  Occupancy             Tennessee Warbler      shrub -0.2255 0.2762 -0.7851 -0.2195  0.3234 1.0017 1200 -0.6912  0.2229
## 712  Occupancy                  Tree Swallow      shrub -0.3713 0.2619 -0.9140 -0.3635  0.1354 1.0051 1328 -0.8268  0.0420
## 713  Occupancy               Tufted Titmouse      shrub  0.0079 0.2498 -0.4610 -0.0036  0.4933 1.0050 1200 -0.3983  0.4284
## 714  Occupancy                Turkey Vulture      shrub -0.2174 0.2571 -0.7043 -0.2267  0.3119 1.0070 1200 -0.6413  0.2125
## 715  Occupancy                         Veery      shrub  0.0130 0.2269 -0.4198  0.0064  0.4804 1.0006 1200 -0.3504  0.3938
## 716  Occupancy                 Virginia Rail      shrub -0.2187 0.2742 -0.7526 -0.2180  0.3047 1.0058 1200 -0.6495  0.2239
## 717  Occupancy                Warbling Vireo      shrub -0.4631 0.2184 -0.9239 -0.4587 -0.0538 1.0013 1200 -0.8282 -0.1367
## 718  Occupancy       White-breasted Nuthatch      shrub -0.0857 0.2505 -0.5442 -0.0976  0.4129 1.0027 1030 -0.4897  0.3316
## 719  Occupancy              White-eyed Vireo      shrub -0.1649 0.2653 -0.6810 -0.1688  0.3690 1.0029  954 -0.5873  0.2887
## 720  Occupancy             Willow Flycatcher      shrub -0.2093 0.2414 -0.6819 -0.2038  0.2899 0.9996 1200 -0.6002  0.1953
## 721  Occupancy                   Wild Turkey      shrub -0.3364 0.2702 -0.8785 -0.3427  0.2017 1.0047 1199 -0.7689  0.1152
## 722  Occupancy                   Winter Wren      shrub -0.1385 0.2633 -0.6456 -0.1421  0.3564 1.0060 1200 -0.5622  0.2806
## 723  Occupancy                     Wood Duck      shrub -0.1863 0.2668 -0.7324 -0.1882  0.3155 1.0001 1200 -0.6305  0.2368
## 724  Occupancy                   Wood Thrush      shrub  0.0277 0.2005 -0.3582  0.0163  0.4550 0.9999 1196 -0.2834  0.3716
## 725  Occupancy          Yellow-billed Cuckoo      shrub -0.2525 0.2578 -0.7884 -0.2430  0.2319 1.0031 1200 -0.6771  0.1689
## 726  Occupancy                Yellow Warbler      shrub -0.3709 0.2056 -0.7947 -0.3628  0.0194 1.0148 1200 -0.7077 -0.0559
## 727  Occupancy         Yellow-throated Vireo      shrub -0.1329 0.2367 -0.5891 -0.1348  0.3673 1.0077 1200 -0.5157  0.2452
## 728  Occupancy       Yellow-throated Warbler      shrub -0.1720 0.2577 -0.6900 -0.1717  0.3249 1.0036 1200 -0.5908  0.2602
## 729  Occupancy            Acadian Flycatcher      hydro -0.0878 0.1902 -0.4553 -0.0827  0.2568 1.0024 1386 -0.4065  0.2153
## 730  Occupancy              Alder Flycatcher      hydro  0.1658 0.2093 -0.2796  0.1760  0.5766 1.0041 1200 -0.1813  0.4985
## 731  Occupancy                 American Crow      hydro  0.1915 0.1774 -0.1398  0.1916  0.5269 1.0004 1200 -0.1005  0.4744
## 732  Occupancy            American Goldfinch      hydro  0.2441 0.1993 -0.1322  0.2398  0.6537 1.0021 1510 -0.0730  0.5722
## 733  Occupancy              American Kestrel      hydro  0.1632 0.2127 -0.2460  0.1721  0.5614 1.0065 1200 -0.2051  0.4940
## 734  Occupancy             American Redstart      hydro  0.2026 0.1887 -0.1458  0.2079  0.5653 1.0013 1200 -0.0997  0.4992
## 735  Occupancy                American Robin      hydro  0.2465 0.1962 -0.1155  0.2421  0.6603 1.0119 1200 -0.0686  0.5831
## 736  Occupancy             American Woodcock      hydro  0.1737 0.2182 -0.2436  0.1779  0.6071 1.0041 1200 -0.1665  0.5292
## 737  Occupancy                    Barred Owl      hydro  0.1325 0.2094 -0.2810  0.1324  0.5255 1.0330  985 -0.2051  0.4674
## 738  Occupancy                    Bald Eagle      hydro  0.1971 0.2081 -0.2031  0.1971  0.6197 1.0087 1200 -0.1339  0.5424
## 739  Occupancy                  Bank Swallow      hydro  0.2230 0.2178 -0.1997  0.2205  0.6646 1.0030 1200 -0.1317  0.5854
## 740  Occupancy              Baltimore Oriole      hydro  0.3364 0.1825 -0.0071  0.3402  0.7166 1.0001 1370  0.0473  0.6569
## 741  Occupancy                  Barn Swallow      hydro  0.2408 0.1973 -0.1535  0.2435  0.6169 1.0105 1200 -0.0875  0.5659
## 742  Occupancy        Black-capped Chickadee      hydro  0.2409 0.2053 -0.1532  0.2327  0.6405 1.0058 1333 -0.0684  0.5663
## 743  Occupancy             Belted Kingfisher      hydro  0.3202 0.1912 -0.0502  0.3165  0.6903 1.0196 1200  0.0007  0.6279
## 744  Occupancy         Blue-gray Gnatcatcher      hydro  0.1984 0.1896 -0.1619  0.1912  0.5875 0.9998 1312 -0.1000  0.5221
## 745  Occupancy          Brown-headed Cowbird      hydro  0.1889 0.2033 -0.2037  0.1932  0.5765 1.0030 1200 -0.1305  0.4985
## 746  Occupancy             Blue-headed Vireo      hydro  0.2483 0.2179 -0.1841  0.2452  0.6900 1.0045 1032 -0.1087  0.5889
## 747  Occupancy                      Blue Jay      hydro  0.1976 0.1892 -0.1724  0.2040  0.5561 1.0001 1200 -0.1131  0.4953
## 748  Occupancy                      Bobolink      hydro  0.1912 0.2099 -0.2347  0.1977  0.6072 1.0128 1510 -0.1564  0.5438
## 749  Occupancy                 Brown Creeper      hydro  0.2461 0.1949 -0.1377  0.2428  0.6350 1.0008 1200 -0.0599  0.5652
## 750  Occupancy                Brown Thrasher      hydro  0.1535 0.1966 -0.2431  0.1540  0.5361 1.0218 1069 -0.1824  0.4713
## 751  Occupancy  Black-throated Green Warbler      hydro  0.2076 0.2236 -0.2283  0.1970  0.6692 1.0006 1360 -0.1441  0.5904
## 752  Occupancy             Broad-winged Hawk      hydro  0.1729 0.2007 -0.2153  0.1706  0.5641 1.0003 1229 -0.1479  0.4970
## 753  Occupancy           Blue-winged Warbler      hydro  0.1423 0.1999 -0.2893  0.1453  0.5336 1.0003 1237 -0.1983  0.4684
## 754  Occupancy                  Canada Goose      hydro  0.2401 0.2015 -0.1514  0.2374  0.6581 1.0147 1200 -0.0803  0.5576
## 755  Occupancy                 Carolina Wren      hydro  0.2774 0.1763 -0.0684  0.2774  0.6266 1.0056 1200 -0.0121  0.5666
## 756  Occupancy                 Cedar Waxwing      hydro  0.1506 0.1773 -0.2134  0.1556  0.4900 1.0043 1200 -0.1419  0.4305
## 757  Occupancy              Cerulean Warbler      hydro  0.2000 0.2207 -0.2690  0.2019  0.6102 1.0013 1360 -0.1641  0.5467
## 758  Occupancy              Chipping Sparrow      hydro  0.1584 0.1874 -0.2394  0.1681  0.5009 1.0036 1099 -0.1552  0.4483
## 759  Occupancy                 Chimney Swift      hydro  0.1057 0.1967 -0.2811  0.1104  0.4990 1.0362 1200 -0.2288  0.4179
## 760  Occupancy                 Cliff Swallow      hydro  0.1756 0.2129 -0.2573  0.1818  0.5931 1.0103 1200 -0.1705  0.5120
## 761  Occupancy                Common Grackle      hydro  0.1510 0.1905 -0.2409  0.1547  0.5205 1.0004 1200 -0.1598  0.4581
## 762  Occupancy                 Cooper's Hawk      hydro  0.1197 0.2021 -0.3083  0.1290  0.4874 1.0067 1333 -0.2303  0.4331
## 763  Occupancy           Common Yellowthroat      hydro  0.4487 0.1752  0.1219  0.4481  0.7919 1.0043 1200  0.1725  0.7419
## 764  Occupancy               Dark-eyed Junco      hydro  0.1070 0.1964 -0.3040  0.1143  0.4735 1.0093 1422 -0.2308  0.4192
## 765  Occupancy              Downy Woodpecker      hydro  0.2397 0.2029 -0.1702  0.2416  0.6217 1.0060 1200 -0.0919  0.5703
## 766  Occupancy              Eastern Bluebird      hydro  0.2293 0.1907 -0.1238  0.2321  0.6148 1.0022 1818 -0.0852  0.5540
## 767  Occupancy              Eastern Kingbird      hydro  0.2801 0.1942 -0.0914  0.2842  0.6740 1.0024 1355 -0.0325  0.6030
## 768  Occupancy            Eastern Meadowlark      hydro  0.2403 0.2058 -0.1771  0.2401  0.6557 1.0010 1200 -0.1084  0.5619
## 769  Occupancy                Eastern Phoebe      hydro  0.2117 0.1870 -0.1559  0.2065  0.6083 1.0028 1200 -0.0793  0.5250
## 770  Occupancy                Eastern Towhee      hydro  0.1978 0.1756 -0.1438  0.2027  0.5498 1.0046 1075 -0.0923  0.4717
## 771  Occupancy            Eastern Wood-Pewee      hydro  0.1924 0.1857 -0.1758  0.1860  0.5568 1.0014 1200 -0.1161  0.4893
## 772  Occupancy             European Starling      hydro  0.1414 0.1838 -0.2344  0.1397  0.4964 1.0004 1200 -0.1649  0.4381
## 773  Occupancy                 Field Sparrow      hydro  0.0604 0.1978 -0.3279  0.0671  0.4267 1.0041 1200 -0.2671  0.3721
## 774  Occupancy              Great Blue Heron      hydro  0.2430 0.2006 -0.1506  0.2442  0.6434 1.0077 1200 -0.0917  0.5798
## 775  Occupancy      Great Crested Flycatcher      hydro  0.2345 0.1891 -0.1171  0.2350  0.5991 1.0078 1200 -0.0527  0.5460
## 776  Occupancy              Great Horned Owl      hydro  0.2157 0.2113 -0.2072  0.2171  0.6230 1.0038 1200 -0.1406  0.5609
## 777  Occupancy                  Gray Catbird      hydro  0.3357 0.1776 -0.0015  0.3289  0.6947 1.0123 1200  0.0409  0.6375
## 778  Occupancy                   Green Heron      hydro  0.2278 0.2146 -0.2061  0.2270  0.6630 1.0039 1200 -0.1307  0.5678
## 779  Occupancy              Hairy Woodpecker      hydro  0.1327 0.2120 -0.3026  0.1296  0.5495 1.0054 1200 -0.2089  0.4720
## 780  Occupancy                  Herring Gull      hydro  0.2644 0.2113 -0.1554  0.2660  0.6737 1.0085  900 -0.0799  0.5971
## 781  Occupancy                 Hermit Thrush      hydro  0.1700 0.2102 -0.2697  0.1796  0.5530 1.0103 1047 -0.2011  0.5049
## 782  Occupancy                   House Finch      hydro  0.2528 0.2028 -0.1515  0.2511  0.6524 1.0071 1200 -0.0625  0.5814
## 783  Occupancy                 House Sparrow      hydro  0.1617 0.1884 -0.2083  0.1630  0.5154 1.0010  816 -0.1426  0.4606
## 784  Occupancy                Hooded Warbler      hydro  0.1002 0.1709 -0.2304  0.1079  0.4118 1.0149 1200 -0.1857  0.3843
## 785  Occupancy                    House Wren      hydro  0.1485 0.1636 -0.1792  0.1483  0.4614 1.0117 1399 -0.1176  0.4149
## 786  Occupancy                Indigo Bunting      hydro  0.4160 0.1784  0.0841  0.4103  0.7915 1.0024 1200  0.1372  0.7189
## 787  Occupancy                      Killdeer      hydro  0.2915 0.1807 -0.0502  0.2813  0.6589 1.0014 1200  0.0214  0.5887
## 788  Occupancy         Louisiana Waterthrush      hydro  0.2552 0.1811 -0.1027  0.2521  0.6082 1.0079 1200 -0.0361  0.5575
## 789  Occupancy                       Mallard      hydro  0.0999 0.2137 -0.3247  0.1091  0.4936 1.0073 1200 -0.2632  0.4352
## 790  Occupancy                 Mourning Dove      hydro  0.3233 0.1889 -0.0408  0.3222  0.6927 1.0216 1102  0.0210  0.6363
## 791  Occupancy             Northern Cardinal      hydro  0.1815 0.1965 -0.2107  0.1765  0.5657 1.0126 1200 -0.1352  0.5076
## 792  Occupancy              Northern Flicker      hydro  0.2084 0.2027 -0.1807  0.2036  0.6126 1.0035 1200 -0.1166  0.5356
## 793  Occupancy               Northern Parula      hydro  0.1581 0.2140 -0.2737  0.1652  0.5845 1.0419 1200 -0.1946  0.4982
## 794  Occupancy Northern Rough-winged Swallow      hydro  0.1171 0.2043 -0.3143  0.1179  0.5028 1.0008 1200 -0.2215  0.4506
## 795  Occupancy                Orchard Oriole      hydro  0.1127 0.1973 -0.3073  0.1162  0.4830 1.0004 1369 -0.2016  0.4339
## 796  Occupancy                      Ovenbird      hydro  0.1182 0.1953 -0.2826  0.1239  0.4888 1.0048 1384 -0.2088  0.4342
## 797  Occupancy           Pileated Woodpecker      hydro  0.1617 0.2138 -0.2692  0.1615  0.6088 1.0058 1200 -0.1823  0.5334
## 798  Occupancy                  Purple Finch      hydro  0.2356 0.2096 -0.1680  0.2329  0.6573 1.0011 1200 -0.1007  0.5831
## 799  Occupancy                 Purple Martin      hydro  0.1989 0.2071 -0.2182  0.2029  0.6017 1.0015 1200 -0.1322  0.5372
## 800  Occupancy        Rose-breasted Grosbeak      hydro  0.2347 0.1787 -0.1137  0.2335  0.5857 1.0054 1200 -0.0660  0.5363
## 801  Occupancy              Ring-billed Gull      hydro  0.1737 0.1894 -0.2170  0.1711  0.5151 1.0048 1200 -0.1508  0.4707
## 802  Occupancy         Red-breasted Nuthatch      hydro  0.2302 0.2097 -0.1907  0.2247  0.6576 1.0004 1200 -0.1029  0.5812
## 803  Occupancy        Red-bellied Woodpecker      hydro  0.2319 0.2012 -0.1619  0.2288  0.6325 0.9991 1200 -0.0955  0.5642
## 804  Occupancy                Red-eyed Vireo      hydro  0.1746 0.1922 -0.2013  0.1708  0.5603 1.0043 1200 -0.1317  0.4894
## 805  Occupancy         Red-headed Woodpecker      hydro  0.1419 0.2013 -0.2753  0.1429  0.5274 1.0016 1248 -0.1865  0.4674
## 806  Occupancy                   Rock Pigeon      hydro  0.1458 0.2129 -0.2816  0.1590  0.5418 1.0130 1200 -0.2100  0.4761
## 807  Occupancy           Red-shouldered Hawk      hydro  0.1729 0.2201 -0.2766  0.1710  0.6143 1.0004 1200 -0.1936  0.5296
## 808  Occupancy               Red-tailed Hawk      hydro  0.0917 0.2028 -0.3257  0.0997  0.4589 1.0126 1090 -0.2578  0.4103
## 809  Occupancy     Ruby-throated Hummingbird      hydro  0.2074 0.2144 -0.2081  0.2153  0.6223 1.0032  592 -0.1397  0.5508
## 810  Occupancy          Red-winged Blackbird      hydro  0.1501 0.1584 -0.1750  0.1541  0.4636 0.9994 1200 -0.1113  0.4095
## 811  Occupancy              Savannah Sparrow      hydro  0.1585 0.2203 -0.2973  0.1607  0.5909 1.0249 1200 -0.2074  0.5039
## 812  Occupancy               Scarlet Tanager      hydro  0.2320 0.1847 -0.1377  0.2277  0.5840 1.0008 1200 -0.0683  0.5305
## 813  Occupancy                  Song Sparrow      hydro  0.4400 0.1670  0.1295  0.4341  0.7854 1.0088 1200  0.1783  0.7316
## 814  Occupancy                 Swamp Sparrow      hydro  0.2662 0.1893 -0.0996  0.2658  0.6470 1.0087 1311 -0.0396  0.5726
## 815  Occupancy             Tennessee Warbler      hydro  0.1954 0.2129 -0.2452  0.1960  0.6083 0.9995 1200 -0.1699  0.5498
## 816  Occupancy                  Tree Swallow      hydro  0.2413 0.1930 -0.1275  0.2407  0.6373 1.0036 1200 -0.0743  0.5681
## 817  Occupancy               Tufted Titmouse      hydro  0.3132 0.2092 -0.0666  0.3007  0.7614 1.0001 1200 -0.0030  0.6692
## 818  Occupancy                Turkey Vulture      hydro  0.1966 0.2126 -0.2111  0.1870  0.6219 1.0387 1200 -0.1498  0.5601
## 819  Occupancy                         Veery      hydro  0.1833 0.1894 -0.1906  0.1875  0.5540 1.0002 1200 -0.1406  0.4756
## 820  Occupancy                 Virginia Rail      hydro  0.2029 0.2109 -0.2254  0.2022  0.5978 1.0083 1200 -0.1465  0.5406
## 821  Occupancy                Warbling Vireo      hydro  0.3372 0.1727 -0.0011  0.3365  0.6814 1.0021 1200  0.0562  0.6210
## 822  Occupancy       White-breasted Nuthatch      hydro  0.2639 0.2023 -0.1288  0.2614  0.6739 1.0088 1200 -0.0607  0.6035
## 823  Occupancy              White-eyed Vireo      hydro  0.2676 0.2111 -0.1483  0.2662  0.6984 1.0074 1035 -0.0780  0.6162
## 824  Occupancy             Willow Flycatcher      hydro  0.2288 0.1863 -0.1310  0.2186  0.6171 1.0009  922 -0.0637  0.5473
## 825  Occupancy                   Wild Turkey      hydro  0.1859 0.2115 -0.2245  0.1885  0.6147 1.0017 1200 -0.1615  0.5194
## 826  Occupancy                   Winter Wren      hydro  0.2023 0.2153 -0.2188  0.2103  0.6041 1.0078 1162 -0.1393  0.5529
## 827  Occupancy                     Wood Duck      hydro  0.2696 0.2036 -0.0974  0.2616  0.6709 1.0004 1187 -0.0614  0.6145
## 828  Occupancy                   Wood Thrush      hydro  0.0881 0.1780 -0.2642  0.0902  0.4473 1.0004 1200 -0.1971  0.3827
## 829  Occupancy          Yellow-billed Cuckoo      hydro  0.2515 0.2063 -0.1439  0.2500  0.6881 1.0035 1200 -0.0923  0.6112
## 830  Occupancy                Yellow Warbler      hydro  0.2212 0.1779 -0.1232  0.2200  0.5793 1.0022 1043 -0.0751  0.5011
## 831  Occupancy         Yellow-throated Vireo      hydro  0.2588 0.2003 -0.1257  0.2590  0.6439 1.0290  950 -0.0614  0.5893
## 832  Occupancy       Yellow-throated Warbler      hydro  0.2197 0.1961 -0.1843  0.2211  0.6056 0.9992 1078 -0.1233  0.5263
## 833  Occupancy            Acadian Flycatcher  subcanopy -0.1797 0.1537 -0.4902 -0.1774  0.1075 0.9995 1200 -0.4494  0.0609
## 834  Occupancy              Alder Flycatcher  subcanopy -0.0276 0.2219 -0.4620 -0.0176  0.3917 1.0002 1200 -0.3908  0.3351
## 835  Occupancy                 American Crow  subcanopy  0.0118 0.1706 -0.2984  0.0105  0.3450 1.0011 1200 -0.2534  0.2892
## 836  Occupancy            American Goldfinch  subcanopy -0.0167 0.2146 -0.4308 -0.0164  0.3978 1.0019 1200 -0.3823  0.3343
## 837  Occupancy              American Kestrel  subcanopy -0.0663 0.2273 -0.5279 -0.0679  0.3583 1.0083 1114 -0.4058  0.2951
## 838  Occupancy             American Redstart  subcanopy -0.0774 0.1983 -0.4940 -0.0696  0.2900 1.0073 1489 -0.4143  0.2358
## 839  Occupancy                American Robin  subcanopy -0.0493 0.1694 -0.3786 -0.0544  0.2981 1.0013 1200 -0.3349  0.2265
## 840  Occupancy             American Woodcock  subcanopy -0.0250 0.2160 -0.4542 -0.0217  0.4068 1.0002 1200 -0.3765  0.3434
## 841  Occupancy                    Barred Owl  subcanopy -0.0951 0.2207 -0.5570 -0.0884  0.3307 1.0021 1478 -0.4686  0.2545
## 842  Occupancy                    Bald Eagle  subcanopy  0.0517 0.2228 -0.3744  0.0507  0.5156 1.0084 1200 -0.3153  0.4308
## 843  Occupancy                  Bank Swallow  subcanopy -0.0687 0.2247 -0.5167 -0.0637  0.3621 1.0074 1200 -0.4221  0.2977
## 844  Occupancy              Baltimore Oriole  subcanopy -0.0343 0.1714 -0.3827 -0.0358  0.3090 1.0103 1200 -0.3165  0.2471
## 845  Occupancy                  Barn Swallow  subcanopy -0.0844 0.2189 -0.5378 -0.0783  0.3228 1.0098 1200 -0.4636  0.2708
## 846  Occupancy        Black-capped Chickadee  subcanopy  0.0542 0.2213 -0.3517  0.0437  0.5198 1.0107 1200 -0.2774  0.4253
## 847  Occupancy             Belted Kingfisher  subcanopy  0.1489 0.1998 -0.2345  0.1423  0.5583 1.0022 1200 -0.1662  0.4756
## 848  Occupancy         Blue-gray Gnatcatcher  subcanopy -0.0579 0.1845 -0.4109 -0.0580  0.2925 1.0024 1200 -0.3560  0.2492
## 849  Occupancy          Brown-headed Cowbird  subcanopy  0.1484 0.1928 -0.1970  0.1324  0.5648 0.9992 1200 -0.1440  0.4879
## 850  Occupancy             Blue-headed Vireo  subcanopy  0.0100 0.2202 -0.4164  0.0097  0.4546 1.0010 1200 -0.3554  0.3736
## 851  Occupancy                      Blue Jay  subcanopy -0.1454 0.1950 -0.5325 -0.1502  0.2500 1.0015 1200 -0.4634  0.1838
## 852  Occupancy                      Bobolink  subcanopy -0.0366 0.2325 -0.4957 -0.0420  0.4412 1.0077 1336 -0.4122  0.3587
## 853  Occupancy                 Brown Creeper  subcanopy  0.0897 0.1942 -0.2724  0.0778  0.4965 1.0025 1200 -0.2160  0.4279
## 854  Occupancy                Brown Thrasher  subcanopy -0.1000 0.2338 -0.5700 -0.0954  0.3553 1.0008 1109 -0.4798  0.2723
## 855  Occupancy  Black-throated Green Warbler  subcanopy -0.0277 0.2293 -0.4891 -0.0223  0.4168 1.0162 1200 -0.3996  0.3464
## 856  Occupancy             Broad-winged Hawk  subcanopy  0.0588 0.2189 -0.3651  0.0577  0.5078 1.0118 1200 -0.2920  0.4174
## 857  Occupancy           Blue-winged Warbler  subcanopy -0.0965 0.2152 -0.5227 -0.0975  0.3332 1.0028 1200 -0.4395  0.2500
## 858  Occupancy                  Canada Goose  subcanopy  0.0468 0.2210 -0.3671  0.0346  0.5090 0.9993 1200 -0.3092  0.4228
## 859  Occupancy                 Carolina Wren  subcanopy  0.1038 0.1837 -0.2397  0.0988  0.4772 1.0061 1200 -0.1796  0.4130
## 860  Occupancy                 Cedar Waxwing  subcanopy -0.0920 0.1736 -0.4483 -0.0891  0.2385 1.0074 1200 -0.3869  0.2022
## 861  Occupancy              Cerulean Warbler  subcanopy -0.0491 0.2227 -0.4755 -0.0416  0.3975 1.0049 1200 -0.4024  0.3138
## 862  Occupancy              Chipping Sparrow  subcanopy -0.1371 0.1839 -0.4998 -0.1410  0.2324 1.0162 1200 -0.4437  0.1737
## 863  Occupancy                 Chimney Swift  subcanopy -0.0230 0.1970 -0.4238 -0.0253  0.3720 1.0005 1200 -0.3463  0.3020
## 864  Occupancy                 Cliff Swallow  subcanopy -0.0683 0.2278 -0.4935 -0.0696  0.3773 1.0011 1200 -0.4293  0.3113
## 865  Occupancy                Common Grackle  subcanopy -0.0541 0.1821 -0.4069 -0.0560  0.3115 1.0086 1386 -0.3533  0.2291
## 866  Occupancy                 Cooper's Hawk  subcanopy -0.1648 0.2146 -0.5918 -0.1600  0.2334 1.0124 1200 -0.5301  0.1745
## 867  Occupancy           Common Yellowthroat  subcanopy -0.0988 0.1646 -0.4215 -0.0935  0.2050 1.0029 1200 -0.3782  0.1627
## 868  Occupancy               Dark-eyed Junco  subcanopy -0.0093 0.1760 -0.3652 -0.0076  0.3271 1.0032 1200 -0.3032  0.2734
## 869  Occupancy              Downy Woodpecker  subcanopy  0.1032 0.2147 -0.2807  0.0970  0.5547 1.0044 1200 -0.2252  0.4768
## 870  Occupancy              Eastern Bluebird  subcanopy -0.1227 0.2071 -0.5588 -0.1127  0.2630 0.9997 1200 -0.4689  0.2042
## 871  Occupancy              Eastern Kingbird  subcanopy -0.1541 0.2158 -0.6016 -0.1480  0.2470 1.0037 1320 -0.5255  0.1804
## 872  Occupancy            Eastern Meadowlark  subcanopy -0.0843 0.2250 -0.5421 -0.0780  0.3717 1.0094 1200 -0.4726  0.2739
## 873  Occupancy                Eastern Phoebe  subcanopy  0.0022 0.1791 -0.3393 -0.0018  0.3619 1.0075 1270 -0.2857  0.3014
## 874  Occupancy                Eastern Towhee  subcanopy -0.0434 0.1847 -0.4072 -0.0455  0.3325 1.0017 1200 -0.3332  0.2597
## 875  Occupancy            Eastern Wood-Pewee  subcanopy  0.0439 0.2093 -0.3406  0.0244  0.4888 1.0017 1200 -0.2816  0.4054
## 876  Occupancy             European Starling  subcanopy -0.1205 0.1900 -0.5235 -0.1161  0.2348 1.0023 1235 -0.4416  0.1834
## 877  Occupancy                 Field Sparrow  subcanopy -0.1320 0.2091 -0.5922 -0.1185  0.2467 1.0011 1200 -0.5098  0.1975
## 878  Occupancy              Great Blue Heron  subcanopy  0.0124 0.1990 -0.3587  0.0054  0.4090 1.0074 1200 -0.3118  0.3496
## 879  Occupancy      Great Crested Flycatcher  subcanopy -0.0181 0.2274 -0.4402 -0.0268  0.4489 1.0136 1321 -0.3895  0.3573
## 880  Occupancy              Great Horned Owl  subcanopy -0.0579 0.2306 -0.5291 -0.0576  0.3968 1.0092 1084 -0.4357  0.3092
## 881  Occupancy                  Gray Catbird  subcanopy  0.0689 0.1541 -0.2179  0.0644  0.3746 1.0072 1058 -0.1782  0.3256
## 882  Occupancy                   Green Heron  subcanopy -0.0718 0.2277 -0.5166 -0.0682  0.3719 1.0016 1200 -0.4556  0.2911
## 883  Occupancy              Hairy Woodpecker  subcanopy  0.1487 0.2290 -0.2695  0.1412  0.6069 1.0072 1200 -0.2059  0.5326
## 884  Occupancy                  Herring Gull  subcanopy  0.1088 0.2221 -0.3017  0.0958  0.5590 1.0012 1200 -0.2336  0.4821
## 885  Occupancy                 Hermit Thrush  subcanopy -0.0460 0.2184 -0.4907 -0.0449  0.3702 1.0022 1321 -0.4138  0.3111
## 886  Occupancy                   House Finch  subcanopy -0.0044 0.2022 -0.4004 -0.0122  0.3874 1.0042 1089 -0.3292  0.3208
## 887  Occupancy                 House Sparrow  subcanopy -0.0678 0.1837 -0.4252 -0.0642  0.2935 1.0081 1200 -0.3736  0.2274
## 888  Occupancy                Hooded Warbler  subcanopy -0.0303 0.1576 -0.3309 -0.0337  0.2927 1.0011 1200 -0.2892  0.2306
## 889  Occupancy                    House Wren  subcanopy -0.0913 0.1487 -0.3867 -0.0877  0.1954 1.0106 1308 -0.3441  0.1574
## 890  Occupancy                Indigo Bunting  subcanopy -0.0563 0.1492 -0.3512 -0.0550  0.2329 1.0107 1200 -0.3029  0.1923
## 891  Occupancy                      Killdeer  subcanopy -0.0642 0.2130 -0.5058 -0.0604  0.3413 1.0006 1200 -0.4281  0.2830
## 892  Occupancy         Louisiana Waterthrush  subcanopy  0.1431 0.1950 -0.2241  0.1345  0.5263 1.0007  925 -0.1657  0.4725
## 893  Occupancy                       Mallard  subcanopy -0.0888 0.2138 -0.5226 -0.0814  0.3132 1.0099 1200 -0.4464  0.2488
## 894  Occupancy                 Mourning Dove  subcanopy -0.1607 0.2005 -0.5822 -0.1532  0.2179 1.0032 1200 -0.5298  0.1655
## 895  Occupancy             Northern Cardinal  subcanopy  0.0009 0.1998 -0.4012 -0.0089  0.4149 1.0021 1200 -0.3235  0.3388
## 896  Occupancy              Northern Flicker  subcanopy -0.0523 0.2066 -0.4552 -0.0551  0.3824 1.0030 1200 -0.3891  0.2902
## 897  Occupancy               Northern Parula  subcanopy  0.0082 0.2199 -0.4177  0.0049  0.4876 1.0019 1200 -0.3351  0.3734
## 898  Occupancy Northern Rough-winged Swallow  subcanopy  0.0101 0.1999 -0.3932  0.0167  0.4019 1.0006 1200 -0.3168  0.3403
## 899  Occupancy                Orchard Oriole  subcanopy -0.0788 0.2112 -0.5037 -0.0762  0.3290 1.0238 1200 -0.4353  0.2629
## 900  Occupancy                      Ovenbird  subcanopy -0.0022 0.1817 -0.3595 -0.0023  0.3749 1.0336 1200 -0.2955  0.3010
## 901  Occupancy           Pileated Woodpecker  subcanopy -0.0327 0.2140 -0.4523 -0.0334  0.4107 1.0012 1371 -0.3752  0.3109
## 902  Occupancy                  Purple Finch  subcanopy -0.0542 0.2207 -0.4872 -0.0547  0.3998 1.0108 1200 -0.4179  0.3142
## 903  Occupancy                 Purple Martin  subcanopy -0.0324 0.2352 -0.5107 -0.0301  0.4360 1.0012 1200 -0.4241  0.3528
## 904  Occupancy        Rose-breasted Grosbeak  subcanopy -0.1170 0.1974 -0.5321 -0.1077  0.2419 0.9994 1200 -0.4605  0.1846
## 905  Occupancy              Ring-billed Gull  subcanopy  0.0945 0.1999 -0.2793  0.0933  0.4976 1.0063 1200 -0.2235  0.4238
## 906  Occupancy         Red-breasted Nuthatch  subcanopy -0.0668 0.2346 -0.5440 -0.0603  0.3815 0.9996 1407 -0.4737  0.2971
## 907  Occupancy        Red-bellied Woodpecker  subcanopy -0.0185 0.2115 -0.4123 -0.0243  0.4060 1.0053 1200 -0.3483  0.3339
## 908  Occupancy                Red-eyed Vireo  subcanopy  0.0959 0.2041 -0.2742  0.0899  0.5152 1.0065 1200 -0.2243  0.4397
## 909  Occupancy         Red-headed Woodpecker  subcanopy  0.0514 0.2126 -0.3686  0.0440  0.4729 0.9993 1200 -0.2823  0.3976
## 910  Occupancy                   Rock Pigeon  subcanopy -0.0971 0.2182 -0.5498 -0.0947  0.3288 0.9998 1200 -0.4652  0.2495
## 911  Occupancy           Red-shouldered Hawk  subcanopy -0.1320 0.2250 -0.5958 -0.1241  0.3025 1.0062 1200 -0.4989  0.2420
## 912  Occupancy               Red-tailed Hawk  subcanopy -0.0993 0.2192 -0.5948 -0.0859  0.3210 1.0009 1262 -0.4660  0.2490
## 913  Occupancy     Ruby-throated Hummingbird  subcanopy  0.0236 0.2330 -0.4180  0.0158  0.5210 1.0051 1050 -0.3338  0.4287
## 914  Occupancy          Red-winged Blackbird  subcanopy -0.3538 0.1988 -0.7722 -0.3414  0.0115 1.0016 1200 -0.6899 -0.0457
## 915  Occupancy              Savannah Sparrow  subcanopy -0.0629 0.2313 -0.5194 -0.0613  0.3762 1.0064 1200 -0.4401  0.3107
## 916  Occupancy               Scarlet Tanager  subcanopy -0.0374 0.2079 -0.4369 -0.0517  0.3756 1.0087 1306 -0.3628  0.3079
## 917  Occupancy                  Song Sparrow  subcanopy -0.1569 0.1517 -0.4589 -0.1549  0.1417 0.9999 1200 -0.4073  0.0920
## 918  Occupancy                 Swamp Sparrow  subcanopy -0.0313 0.2140 -0.4645 -0.0294  0.3887 1.0125 1200 -0.3890  0.3312
## 919  Occupancy             Tennessee Warbler  subcanopy -0.0370 0.2275 -0.4983 -0.0362  0.4024 1.0080 1200 -0.3974  0.3355
## 920  Occupancy                  Tree Swallow  subcanopy -0.0746 0.2129 -0.4931 -0.0685  0.3380 1.0103 1467 -0.4120  0.2681
## 921  Occupancy               Tufted Titmouse  subcanopy -0.1759 0.2276 -0.6121 -0.1775  0.2800 1.0100 1200 -0.5461  0.1928
## 922  Occupancy                Turkey Vulture  subcanopy -0.1717 0.2241 -0.6544 -0.1560  0.2386 1.0013 1121 -0.5667  0.1636
## 923  Occupancy                         Veery  subcanopy  0.1131 0.1965 -0.2427  0.0967  0.5337 1.0028 1200 -0.1970  0.4356
## 924  Occupancy                 Virginia Rail  subcanopy -0.0262 0.2265 -0.4787 -0.0253  0.4498 1.0005 1200 -0.3953  0.3419
## 925  Occupancy                Warbling Vireo  subcanopy -0.0679 0.1799 -0.4380 -0.0666  0.2763 1.0013 1200 -0.3730  0.2292
## 926  Occupancy       White-breasted Nuthatch  subcanopy  0.0808 0.2305 -0.3439  0.0693  0.5781 1.0107 1200 -0.2723  0.4783
## 927  Occupancy              White-eyed Vireo  subcanopy  0.0190 0.2226 -0.4090  0.0169  0.4690 1.0009 1200 -0.3396  0.3748
## 928  Occupancy             Willow Flycatcher  subcanopy -0.0883 0.2119 -0.5212 -0.0823  0.3318 1.0149 1200 -0.4600  0.2486
## 929  Occupancy                   Wild Turkey  subcanopy -0.0889 0.2132 -0.5203 -0.0791  0.3007 1.0068 1116 -0.4426  0.2571
## 930  Occupancy                   Winter Wren  subcanopy -0.0099 0.2119 -0.4147 -0.0077  0.4037 1.0002 1200 -0.3709  0.3326
## 931  Occupancy                     Wood Duck  subcanopy -0.0057 0.2221 -0.4259 -0.0112  0.4642 1.0001 1320 -0.3665  0.3510
## 932  Occupancy                   Wood Thrush  subcanopy  0.0486 0.1945 -0.2948  0.0372  0.4735 1.0022 1200 -0.2544  0.4017
## 933  Occupancy          Yellow-billed Cuckoo  subcanopy -0.0115 0.2214 -0.4658 -0.0141  0.4215 1.0103 1200 -0.3577  0.3657
## 934  Occupancy                Yellow Warbler  subcanopy -0.2363 0.1911 -0.6448 -0.2265  0.0937 1.0028 1200 -0.5579  0.0604
## 935  Occupancy         Yellow-throated Vireo  subcanopy -0.0501 0.2027 -0.4592 -0.0539  0.3456 1.0156 1083 -0.3909  0.2806
## 936  Occupancy       Yellow-throated Warbler  subcanopy -0.1241 0.2164 -0.5827 -0.1133  0.2813 1.0120 1200 -0.4979  0.2159
## 937  Occupancy            Acadian Flycatcher     canopy -0.1580 0.1620 -0.4790 -0.1559  0.1576 1.0029  812 -0.4222  0.1007
## 938  Occupancy              Alder Flycatcher     canopy -0.1485 0.2569 -0.6664 -0.1320  0.3206 1.0087 1200 -0.5839  0.2664
## 939  Occupancy                 American Crow     canopy  0.0381 0.1856 -0.3347  0.0358  0.4040 1.0005 1200 -0.2588  0.3502
## 940  Occupancy            American Goldfinch     canopy  0.0510 0.2291 -0.3841  0.0520  0.5068 1.0061 1200 -0.3205  0.4307
## 941  Occupancy              American Kestrel     canopy  0.1032 0.2566 -0.3701  0.0884  0.6733 1.0018 1200 -0.2935  0.5522
## 942  Occupancy             American Redstart     canopy -0.0599 0.2163 -0.4925 -0.0589  0.3541 1.0015 1200 -0.4220  0.2917
## 943  Occupancy                American Robin     canopy -0.0838 0.2169 -0.5082 -0.0807  0.3331 1.0204 1200 -0.4333  0.2633
## 944  Occupancy             American Woodcock     canopy -0.0919 0.2434 -0.5819 -0.0893  0.3760 1.0022 1200 -0.4972  0.2971
## 945  Occupancy                    Barred Owl     canopy -0.2994 0.2538 -0.8650 -0.2790  0.1441 1.0000 1147 -0.7488  0.0856
## 946  Occupancy                    Bald Eagle     canopy -0.0713 0.2517 -0.5786 -0.0697  0.4242 1.0038 1200 -0.4868  0.3270
## 947  Occupancy                  Bank Swallow     canopy -0.0407 0.2508 -0.5155 -0.0418  0.4929 1.0026 1070 -0.4385  0.3740
## 948  Occupancy              Baltimore Oriole     canopy -0.0883 0.2038 -0.5014 -0.0865  0.3162 1.0022 1200 -0.4347  0.2445
## 949  Occupancy                  Barn Swallow     canopy -0.1564 0.2263 -0.6209 -0.1545  0.2806 1.0081 1200 -0.5348  0.1994
## 950  Occupancy        Black-capped Chickadee     canopy -0.1228 0.2258 -0.5870 -0.1187  0.3262 1.0060 1306 -0.5054  0.2434
## 951  Occupancy             Belted Kingfisher     canopy -0.1104 0.2203 -0.5471 -0.1050  0.3170 1.0077 1200 -0.4779  0.2555
## 952  Occupancy         Blue-gray Gnatcatcher     canopy  0.1333 0.1923 -0.2361  0.1244  0.5107 1.0009 1200 -0.1733  0.4655
## 953  Occupancy          Brown-headed Cowbird     canopy  0.0266 0.1984 -0.3583  0.0299  0.4158 1.0172 1200 -0.3025  0.3552
## 954  Occupancy             Blue-headed Vireo     canopy -0.0693 0.2561 -0.6124 -0.0581  0.4320 1.0052 1532 -0.4963  0.3591
## 955  Occupancy                      Blue Jay     canopy -0.1116 0.1942 -0.5070 -0.1072  0.2713 1.0051 1200 -0.4405  0.2101
## 956  Occupancy                      Bobolink     canopy -0.0624 0.2616 -0.5938 -0.0623  0.4571 0.9998 1200 -0.4750  0.3693
## 957  Occupancy                 Brown Creeper     canopy  0.2121 0.2252 -0.1918  0.2072  0.6749 1.0061 1200 -0.1321  0.5910
## 958  Occupancy                Brown Thrasher     canopy -0.1963 0.2440 -0.7116 -0.1921  0.2447 1.0036 1200 -0.6089  0.1840
## 959  Occupancy  Black-throated Green Warbler     canopy -0.0717 0.2510 -0.5746 -0.0735  0.4234 1.0027 1355 -0.5010  0.3481
## 960  Occupancy             Broad-winged Hawk     canopy -0.1150 0.2523 -0.6274 -0.1100  0.3564 1.0009 1200 -0.5484  0.2856
## 961  Occupancy           Blue-winged Warbler     canopy -0.1614 0.2266 -0.6479 -0.1563  0.2951 1.0069 1200 -0.5484  0.2031
## 962  Occupancy                  Canada Goose     canopy  0.1290 0.2507 -0.3486  0.1175  0.6385 1.0030  782 -0.2603  0.5654
## 963  Occupancy                 Carolina Wren     canopy -0.0711 0.2108 -0.4964 -0.0746  0.3327 1.0012 1105 -0.4203  0.2743
## 964  Occupancy                 Cedar Waxwing     canopy -0.1540 0.1930 -0.5550 -0.1394  0.2139 0.9995 1200 -0.4929  0.1574
## 965  Occupancy              Cerulean Warbler     canopy -0.0704 0.2671 -0.5798 -0.0784  0.4683 0.9996 1100 -0.5056  0.3642
## 966  Occupancy              Chipping Sparrow     canopy  0.0425 0.1857 -0.3248  0.0387  0.4142 1.0025 1416 -0.2627  0.3541
## 967  Occupancy                 Chimney Swift     canopy -0.0842 0.1944 -0.4591 -0.0783  0.2773 1.0046 1200 -0.4099  0.2205
## 968  Occupancy                 Cliff Swallow     canopy -0.2020 0.2485 -0.6985 -0.1983  0.2664 1.0035 1200 -0.6186  0.1906
## 969  Occupancy                Common Grackle     canopy -0.1628 0.2092 -0.5974 -0.1555  0.2374 1.0003 1200 -0.5389  0.1623
## 970  Occupancy                 Cooper's Hawk     canopy -0.0694 0.2324 -0.5375 -0.0730  0.3839 0.9998 1200 -0.4578  0.3108
## 971  Occupancy           Common Yellowthroat     canopy -0.4488 0.1911 -0.8437 -0.4439 -0.0829 1.0061 1200 -0.7723 -0.1436
## 972  Occupancy               Dark-eyed Junco     canopy  0.1920 0.2199 -0.2169  0.1864  0.6408 1.0010 1200 -0.1569  0.5645
## 973  Occupancy              Downy Woodpecker     canopy -0.1148 0.2345 -0.5936 -0.1116  0.3524 1.0056 1200 -0.5097  0.2598
## 974  Occupancy              Eastern Bluebird     canopy -0.1780 0.2063 -0.5769 -0.1700  0.2180 1.0040 1200 -0.5214  0.1663
## 975  Occupancy              Eastern Kingbird     canopy  0.0427 0.2202 -0.3737  0.0401  0.4897 1.0008 1200 -0.3106  0.4112
## 976  Occupancy            Eastern Meadowlark     canopy  0.0549 0.2499 -0.3858  0.0417  0.5953 1.0048 1200 -0.3266  0.4864
## 977  Occupancy                Eastern Phoebe     canopy  0.2521 0.2181 -0.1502  0.2411  0.7134 1.0006 1200 -0.0739  0.6368
## 978  Occupancy                Eastern Towhee     canopy -0.2227 0.1965 -0.6217 -0.2213  0.1575 1.0025 1078 -0.5604  0.0967
## 979  Occupancy            Eastern Wood-Pewee     canopy  0.0380 0.2003 -0.3450  0.0303  0.4225 1.0117 1200 -0.2718  0.3593
## 980  Occupancy             European Starling     canopy  0.0178 0.1854 -0.3714  0.0181  0.3835 1.0001 1200 -0.2855  0.3217
## 981  Occupancy                 Field Sparrow     canopy -0.2603 0.2168 -0.7045 -0.2537  0.1526 1.0037 1200 -0.6259  0.0738
## 982  Occupancy              Great Blue Heron     canopy -0.0457 0.2201 -0.4702 -0.0494  0.4079 1.0059 1200 -0.4050  0.3298
## 983  Occupancy      Great Crested Flycatcher     canopy -0.1468 0.2320 -0.5891 -0.1432  0.3045 1.0100 1114 -0.5290  0.2276
## 984  Occupancy              Great Horned Owl     canopy -0.0926 0.2449 -0.5943 -0.0948  0.3988 1.0081 1200 -0.5056  0.3060
## 985  Occupancy                  Gray Catbird     canopy  0.0478 0.1634 -0.2488  0.0498  0.3756 1.0118 1231 -0.2054  0.3067
## 986  Occupancy                   Green Heron     canopy  0.0087 0.2543 -0.4567 -0.0091  0.5252 1.0055 1338 -0.4004  0.4476
## 987  Occupancy              Hairy Woodpecker     canopy -0.1746 0.2628 -0.6789 -0.1777  0.3299 1.0052 1516 -0.5970  0.2480
## 988  Occupancy                  Herring Gull     canopy -0.0845 0.2500 -0.5926 -0.0816  0.4259 1.0308 1200 -0.4834  0.3214
## 989  Occupancy                 Hermit Thrush     canopy -0.0710 0.2496 -0.5382 -0.0695  0.4295 1.0058 1200 -0.4651  0.3345
## 990  Occupancy                   House Finch     canopy -0.0734 0.2234 -0.5101 -0.0712  0.3815 1.0051 1200 -0.4383  0.2720
## 991  Occupancy                 House Sparrow     canopy  0.1328 0.1837 -0.2271  0.1238  0.5103 1.0000 1200 -0.1643  0.4475
## 992  Occupancy                Hooded Warbler     canopy  0.1317 0.1798 -0.2143  0.1233  0.5096 1.0004 1200 -0.1545  0.4394
## 993  Occupancy                    House Wren     canopy -0.0816 0.1581 -0.3923 -0.0782  0.2340 1.0074 1200 -0.3486  0.1760
## 994  Occupancy                Indigo Bunting     canopy -0.0933 0.1500 -0.3903 -0.0941  0.1945 1.0089 1200 -0.3398  0.1462
## 995  Occupancy                      Killdeer     canopy  0.2610 0.2342 -0.1633  0.2465  0.7737 1.0009 1200 -0.1037  0.6466
## 996  Occupancy         Louisiana Waterthrush     canopy -0.1056 0.2106 -0.5101 -0.1007  0.3157 1.0034 1200 -0.4552  0.2392
## 997  Occupancy                       Mallard     canopy  0.0014 0.2352 -0.4467 -0.0021  0.4868 1.0057 1200 -0.3618  0.3924
## 998  Occupancy                 Mourning Dove     canopy  0.0200 0.1964 -0.3588  0.0196  0.4114 1.0178 1063 -0.2884  0.3581
## 999  Occupancy             Northern Cardinal     canopy -0.3319 0.2165 -0.7627 -0.3256  0.0950 1.0056 1200 -0.6935  0.0231
## 1000 Occupancy              Northern Flicker     canopy -0.0422 0.2238 -0.4807 -0.0393  0.3755 1.0141 1200 -0.3995  0.3273
## 1001 Occupancy               Northern Parula     canopy -0.0510 0.2643 -0.5647 -0.0442  0.4642 0.9995 1337 -0.4708  0.3814
## 1002 Occupancy Northern Rough-winged Swallow     canopy  0.0042 0.2183 -0.4212 -0.0016  0.4295 1.0041 1200 -0.3408  0.3558
## 1003 Occupancy                Orchard Oriole     canopy -0.3400 0.2401 -0.8403 -0.3203  0.0817 1.0172 1200 -0.7609  0.0258
## 1004 Occupancy                      Ovenbird     canopy -0.2391 0.2231 -0.6868 -0.2323  0.1813 1.0004 1314 -0.6106  0.1150
## 1005 Occupancy           Pileated Woodpecker     canopy -0.1712 0.2318 -0.6309 -0.1725  0.2823 1.0011 1012 -0.5524  0.2274
## 1006 Occupancy                  Purple Finch     canopy -0.0123 0.2579 -0.5028 -0.0110  0.4903 1.0023 1200 -0.4131  0.4003
## 1007 Occupancy                 Purple Martin     canopy -0.0675 0.2630 -0.5718 -0.0660  0.4427 0.9991 1403 -0.4863  0.3679
## 1008 Occupancy        Rose-breasted Grosbeak     canopy -0.1090 0.2233 -0.6016 -0.1082  0.3219 1.0025 1463 -0.4680  0.2585
## 1009 Occupancy              Ring-billed Gull     canopy -0.1404 0.2142 -0.5824 -0.1356  0.2789 0.9995 1200 -0.5083  0.2061
## 1010 Occupancy         Red-breasted Nuthatch     canopy -0.0869 0.2592 -0.6057 -0.0788  0.4283 1.0092 1316 -0.5229  0.3320
## 1011 Occupancy        Red-bellied Woodpecker     canopy -0.0230 0.2321 -0.4560 -0.0227  0.4409 1.0024 1200 -0.3777  0.3555
## 1012 Occupancy                Red-eyed Vireo     canopy -0.0717 0.1924 -0.4753 -0.0691  0.2999 1.0183 1207 -0.3985  0.2351
## 1013 Occupancy         Red-headed Woodpecker     canopy -0.0533 0.2385 -0.5380 -0.0561  0.4084 1.0081 1200 -0.4366  0.3301
## 1014 Occupancy                   Rock Pigeon     canopy  0.1152 0.2619 -0.3733  0.1042  0.6591 1.0049 1443 -0.2881  0.5610
## 1015 Occupancy           Red-shouldered Hawk     canopy -0.1580 0.2635 -0.6879 -0.1638  0.3253 1.0229 1091 -0.5800  0.2460
## 1016 Occupancy               Red-tailed Hawk     canopy -0.0367 0.2278 -0.4833 -0.0432  0.4208 1.0295 1081 -0.3883  0.3583
## 1017 Occupancy     Ruby-throated Hummingbird     canopy -0.1287 0.2597 -0.6471 -0.1271  0.3563 0.9998 1200 -0.5704  0.2929
## 1018 Occupancy          Red-winged Blackbird     canopy -0.0761 0.1570 -0.3853 -0.0761  0.2258 1.0139 1074 -0.3460  0.1844
## 1019 Occupancy              Savannah Sparrow     canopy  0.1111 0.2605 -0.3451  0.0932  0.6549 1.0017 1343 -0.2806  0.5563
## 1020 Occupancy               Scarlet Tanager     canopy -0.2044 0.2039 -0.5768 -0.2108  0.2081 0.9992 1401 -0.5306  0.1408
## 1021 Occupancy                  Song Sparrow     canopy -0.0516 0.1579 -0.3775 -0.0478  0.2554 1.0026 1289 -0.3205  0.2017
## 1022 Occupancy                 Swamp Sparrow     canopy -0.3165 0.2358 -0.8034 -0.3074  0.1251 1.0011 1200 -0.7182  0.0538
## 1023 Occupancy             Tennessee Warbler     canopy -0.0657 0.2580 -0.6022 -0.0612  0.4382 1.0041 1077 -0.4924  0.3550
## 1024 Occupancy                  Tree Swallow     canopy -0.2351 0.2198 -0.6943 -0.2300  0.1604 1.0014 1200 -0.5920  0.1122
## 1025 Occupancy               Tufted Titmouse     canopy -0.1127 0.2208 -0.5555 -0.1127  0.3076 1.0079 1200 -0.4822  0.2365
## 1026 Occupancy                Turkey Vulture     canopy -0.0946 0.2189 -0.5164 -0.0953  0.3176 1.0027 1200 -0.4479  0.2664
## 1027 Occupancy                         Veery     canopy  0.0132 0.2298 -0.4363  0.0182  0.4544 1.0076 1200 -0.3688  0.3801
## 1028 Occupancy                 Virginia Rail     canopy -0.0706 0.2551 -0.5890 -0.0699  0.4251 1.0008 1200 -0.4722  0.3566
## 1029 Occupancy                Warbling Vireo     canopy  0.0484 0.1852 -0.3046  0.0434  0.4288 1.0034 1200 -0.2530  0.3684
## 1030 Occupancy       White-breasted Nuthatch     canopy -0.1758 0.2436 -0.6842 -0.1652  0.3070 1.0043 1200 -0.5782  0.2175
## 1031 Occupancy              White-eyed Vireo     canopy -0.1261 0.2501 -0.6581 -0.1226  0.3596 1.0018 1200 -0.5560  0.2869
## 1032 Occupancy             Willow Flycatcher     canopy -0.2775 0.2234 -0.7334 -0.2740  0.1421 1.0006 1200 -0.6551  0.0948
## 1033 Occupancy                   Wild Turkey     canopy -0.0113 0.2409 -0.4831 -0.0101  0.4480 0.9998 1200 -0.4038  0.3819
## 1034 Occupancy                   Winter Wren     canopy  0.0038 0.2405 -0.4447 -0.0115  0.4937 1.0051 1200 -0.3708  0.4059
## 1035 Occupancy                     Wood Duck     canopy -0.1555 0.2488 -0.6683 -0.1484  0.3244 1.0129 1200 -0.5825  0.2488
## 1036 Occupancy                   Wood Thrush     canopy -0.0673 0.1721 -0.3899 -0.0717  0.2692 1.0180 1200 -0.3453  0.2098
## 1037 Occupancy          Yellow-billed Cuckoo     canopy -0.1405 0.2473 -0.6289 -0.1282  0.3419 1.0047 1331 -0.5516  0.2620
## 1038 Occupancy                Yellow Warbler     canopy -0.0924 0.1795 -0.4323 -0.0842  0.2456 1.0170 1052 -0.3847  0.1920
## 1039 Occupancy         Yellow-throated Vireo     canopy  0.1148 0.2352 -0.3425  0.1079  0.5876 1.0033 1200 -0.2604  0.4957
## 1040 Occupancy       Yellow-throated Warbler     canopy -0.0787 0.2414 -0.5609 -0.0815  0.4042 1.0109 1100 -0.4773  0.3197
## 1041 Detection            Acadian Flycatcher  Intercept  0.8643 0.1472  0.5837  0.8627  1.1588 1.0117 1200  0.6268  1.1074
## 1042 Detection              Alder Flycatcher  Intercept -1.6741 1.1155 -3.9022 -1.6506  0.3571 1.0045  729 -3.5421  0.0867
## 1043 Detection                 American Crow  Intercept -0.6797 0.2610 -1.2134 -0.6687 -0.1782 1.0233 1096 -1.1106 -0.2599
## 1044 Detection            American Goldfinch  Intercept  0.0759 0.1251 -0.1692  0.0754  0.3178 1.0038 1407 -0.1255  0.2774
## 1045 Detection              American Kestrel  Intercept -1.6279 1.1333 -3.8276 -1.6246  0.5440 0.9994  738 -3.4474  0.1391
## 1046 Detection             American Redstart  Intercept -0.9466 0.5703 -2.1727 -0.9210  0.0832 1.0114 1200 -1.9214 -0.0462
## 1047 Detection                American Robin  Intercept  0.9939 0.1206  0.7597  0.9922  1.2358 1.0026 1200  0.7997  1.1941
## 1048 Detection             American Woodcock  Intercept -0.9530 0.9482 -2.9104 -0.9113  0.8569 1.0032  990 -2.5889  0.5041
## 1049 Detection                    Barred Owl  Intercept -2.1231 0.9325 -4.0167 -2.1114 -0.2796 1.0287  590 -3.6258 -0.5466
## 1050 Detection                    Bald Eagle  Intercept -1.9964 0.9420 -3.9578 -1.9620 -0.2381 1.0073  627 -3.6670 -0.5114
## 1051 Detection                  Bank Swallow  Intercept -1.7574 0.9713 -3.7881 -1.7247  0.1171 1.0188  854 -3.3810 -0.1768
## 1052 Detection              Baltimore Oriole  Intercept -0.7448 0.2110 -1.1841 -0.7332 -0.3466 1.0031 1200 -1.0935 -0.4098
## 1053 Detection                  Barn Swallow  Intercept -1.6559 0.6026 -2.9254 -1.6084 -0.6129 0.9993  845 -2.7301 -0.7499
## 1054 Detection        Black-capped Chickadee  Intercept  0.0757 0.1115 -0.1376  0.0746  0.2951 1.0012 1200 -0.1076  0.2604
## 1055 Detection             Belted Kingfisher  Intercept -1.8563 0.4920 -2.7989 -1.8545 -0.9245 1.0032  967 -2.6586 -1.0701
## 1056 Detection         Blue-gray Gnatcatcher  Intercept -0.4660 0.1551 -0.7626 -0.4674 -0.1493 1.0008 1200 -0.7226 -0.2045
## 1057 Detection          Brown-headed Cowbird  Intercept -0.1625 0.1293 -0.4125 -0.1628  0.0896 1.0002 1200 -0.3750  0.0481
## 1058 Detection             Blue-headed Vireo  Intercept -1.7868 1.1225 -4.1819 -1.7279  0.2893 1.0074  838 -3.7578  0.0027
## 1059 Detection                      Blue Jay  Intercept  0.5165 0.1248  0.2701  0.5119  0.7618 1.0070  984  0.3161  0.7210
## 1060 Detection                      Bobolink  Intercept -1.4705 1.3344 -4.1477 -1.4097  1.0013 1.0049  992 -3.6925  0.5897
## 1061 Detection                 Brown Creeper  Intercept -1.1108 0.4489 -2.0195 -1.0909 -0.2722 1.0113 1200 -1.8631 -0.3894
## 1062 Detection                Brown Thrasher  Intercept -1.8445 0.7174 -3.2452 -1.8389 -0.4842 1.0006 1007 -3.0059 -0.6584
## 1063 Detection  Black-throated Green Warbler  Intercept -1.4131 1.2808 -4.0164 -1.3846  0.9837 1.0108  862 -3.5002  0.6086
## 1064 Detection             Broad-winged Hawk  Intercept -1.8369 0.9920 -3.7905 -1.7817 -0.0117 1.0001  777 -3.4760 -0.2393
## 1065 Detection           Blue-winged Warbler  Intercept -1.2623 0.7312 -2.8296 -1.1972  0.0600 1.0160  838 -2.5011 -0.0892
## 1066 Detection                  Canada Goose  Intercept -2.4707 0.6821 -3.7220 -2.4716 -1.1015 1.0257  495 -3.5952 -1.3152
## 1067 Detection                 Carolina Wren  Intercept -0.9941 0.2265 -1.4481 -0.9977 -0.5628 1.0212 1357 -1.3749 -0.6213
## 1068 Detection                 Cedar Waxwing  Intercept -0.7265 0.2102 -1.1252 -0.7273 -0.3037 1.0007 1200 -1.0652 -0.3833
## 1069 Detection              Cerulean Warbler  Intercept -1.4238 1.2630 -3.9153 -1.4236  1.0922 1.0155  778 -3.4978  0.6124
## 1070 Detection              Chipping Sparrow  Intercept -1.0054 0.3707 -1.7857 -0.9934 -0.3435 1.0006 1200 -1.6522 -0.4145
## 1071 Detection                 Chimney Swift  Intercept -0.9357 0.2142 -1.3594 -0.9382 -0.5245 1.0024 1027 -1.2937 -0.5787
## 1072 Detection                 Cliff Swallow  Intercept -1.8367 1.0922 -4.0150 -1.8012  0.1658 1.0030  639 -3.6981 -0.1208
## 1073 Detection                Common Grackle  Intercept -1.1873 0.2294 -1.6391 -1.1950 -0.7279 1.0128 1380 -1.5606 -0.8116
## 1074 Detection                 Cooper's Hawk  Intercept -1.2478 0.6727 -2.6828 -1.2280  0.0787 1.0016 1235 -2.4540 -0.2002
## 1075 Detection           Common Yellowthroat  Intercept  0.1028 0.2097 -0.3049  0.1085  0.5048 1.0355 1357 -0.2395  0.4558
## 1076 Detection               Dark-eyed Junco  Intercept -0.9113 0.4098 -1.7383 -0.8948 -0.1659 0.9994 1200 -1.6068 -0.2767
## 1077 Detection              Downy Woodpecker  Intercept -0.0589 0.1286 -0.3064 -0.0586  0.1883 1.0195 1200 -0.2704  0.1512
## 1078 Detection              Eastern Bluebird  Intercept -1.4942 0.3896 -2.2935 -1.4851 -0.7693 1.0166  959 -2.1398 -0.8748
## 1079 Detection              Eastern Kingbird  Intercept -0.4291 0.5149 -1.4336 -0.4211  0.5673 1.0136 1200 -1.2666  0.4599
## 1080 Detection            Eastern Meadowlark  Intercept -0.9043 0.9187 -2.7650 -0.8630  0.7879 1.0029 1320 -2.4745  0.5381
## 1081 Detection                Eastern Phoebe  Intercept -1.1379 0.4401 -2.0233 -1.1184 -0.2874 1.0040 1200 -1.8792 -0.4544
## 1082 Detection                Eastern Towhee  Intercept -0.5204 0.2702 -1.0620 -0.5209 -0.0029 1.0073 1200 -0.9564 -0.0877
## 1083 Detection            Eastern Wood-Pewee  Intercept  1.0280 0.1189  0.7945  1.0212  1.2633 1.0073 1200  0.8374  1.2274
## 1084 Detection             European Starling  Intercept -0.5333 0.3281 -1.1785 -0.5247  0.0905 0.9996 1200 -1.0908 -0.0085
## 1085 Detection                 Field Sparrow  Intercept  0.7355 0.3961 -0.0553  0.7252  1.4843 1.0020 1200  0.0784  1.3697
## 1086 Detection              Great Blue Heron  Intercept -1.8673 0.7224 -3.4583 -1.8091 -0.5656 1.0068  772 -3.1623 -0.7614
## 1087 Detection      Great Crested Flycatcher  Intercept -1.1196 0.1908 -1.4849 -1.1226 -0.7404 1.0131  890 -1.4366 -0.7951
## 1088 Detection              Great Horned Owl  Intercept -1.8683 1.2221 -4.4594 -1.8284  0.4145 1.0121  627 -4.0969  0.0593
## 1089 Detection                  Gray Catbird  Intercept  0.1520 0.1641 -0.1766  0.1560  0.4633 1.0161 1200 -0.1268  0.4172
## 1090 Detection                   Green Heron  Intercept -1.7350 1.1629 -4.0856 -1.7016  0.4264 1.0097  787 -3.7752  0.1287
## 1091 Detection              Hairy Woodpecker  Intercept -1.7415 0.2663 -2.2815 -1.7310 -1.2302 1.0136  841 -2.1851 -1.3014
## 1092 Detection                  Herring Gull  Intercept -0.5064 1.0113 -2.5534 -0.4446  1.3215 0.9999 1200 -2.2683  1.0595
## 1093 Detection                 Hermit Thrush  Intercept  0.5429 0.8029 -1.0748  0.5285  2.1675 1.0013 1200 -0.7537  1.8752
## 1094 Detection                   House Finch  Intercept -1.8377 0.4478 -2.6998 -1.8331 -0.9561 1.0242  890 -2.5746 -1.1312
## 1095 Detection                 House Sparrow  Intercept -0.2962 0.2909 -0.8856 -0.2965  0.2578 1.0000 1327 -0.7742  0.1797
## 1096 Detection                Hooded Warbler  Intercept  0.1753 0.2027 -0.2112  0.1740  0.5865 1.0030 1200 -0.1664  0.5080
## 1097 Detection                    House Wren  Intercept  0.4640 0.1592  0.1455  0.4705  0.7518 0.9993 1200  0.1948  0.7169
## 1098 Detection                Indigo Bunting  Intercept  0.0933 0.1658 -0.2318  0.0970  0.4259 1.0055  983 -0.1754  0.3703
## 1099 Detection                      Killdeer  Intercept -0.9432 0.5912 -2.0994 -0.9184  0.1337 1.0123 1003 -1.9807 -0.0357
## 1100 Detection         Louisiana Waterthrush  Intercept -0.9444 0.5278 -2.0265 -0.9172 -0.0144 1.0078 1200 -1.8706 -0.1276
## 1101 Detection                       Mallard  Intercept -1.8839 0.8827 -3.7381 -1.8007 -0.3214 1.0321  479 -3.4326 -0.5220
## 1102 Detection                 Mourning Dove  Intercept -1.3790 0.3666 -2.0841 -1.3802 -0.6558 1.0101 1200 -1.9927 -0.7894
## 1103 Detection             Northern Cardinal  Intercept  0.8398 0.1182  0.5980  0.8438  1.0679 1.0053 1200  0.6450  1.0357
## 1104 Detection              Northern Flicker  Intercept -1.7088 0.3163 -2.2743 -1.7312 -1.0598 1.0040  787 -2.1830 -1.1682
## 1105 Detection               Northern Parula  Intercept -1.6405 1.0742 -3.8835 -1.6044  0.3293 1.0072  879 -3.4650  0.0158
## 1106 Detection Northern Rough-winged Swallow  Intercept -1.6007 0.6056 -2.8328 -1.5879 -0.4858 1.0021  957 -2.6297 -0.6418
## 1107 Detection                Orchard Oriole  Intercept -1.0196 0.4229 -1.8503 -1.0169 -0.2320 1.0040 1200 -1.7180 -0.2983
## 1108 Detection                      Ovenbird  Intercept -0.2079 0.4510 -1.1550 -0.1855  0.6311 1.0057 1215 -0.9560  0.4868
## 1109 Detection           Pileated Woodpecker  Intercept -1.8097 0.3005 -2.3579 -1.8209 -1.2412 1.0039  742 -2.2907 -1.3123
## 1110 Detection                  Purple Finch  Intercept -1.7235 1.1111 -3.9456 -1.7424  0.5837 1.0187  748 -3.6376  0.0618
## 1111 Detection                 Purple Martin  Intercept -1.5118 1.3291 -4.1105 -1.4958  1.0500 1.0002 1014 -3.7995  0.7071
## 1112 Detection        Rose-breasted Grosbeak  Intercept -1.3327 0.3259 -1.9571 -1.3292 -0.7090 1.0040  855 -1.8789 -0.8033
## 1113 Detection              Ring-billed Gull  Intercept -0.8809 0.5683 -2.0897 -0.8566  0.1216 1.0003  648 -1.8103 -0.0205
## 1114 Detection         Red-breasted Nuthatch  Intercept -1.7810 1.1536 -4.1967 -1.7196  0.2994 1.0022  672 -3.7854  0.0540
## 1115 Detection        Red-bellied Woodpecker  Intercept  0.3512 0.1094  0.1342  0.3522  0.5645 1.0000 1200  0.1724  0.5309
## 1116 Detection                Red-eyed Vireo  Intercept  0.9779 0.1124  0.7648  0.9796  1.2020 1.0021 1446  0.7896  1.1626
## 1117 Detection         Red-headed Woodpecker  Intercept -1.8149 0.8086 -3.5041 -1.7591 -0.3246 1.0018  770 -3.1948 -0.5814
## 1118 Detection                   Rock Pigeon  Intercept -1.7875 0.9944 -3.8305 -1.7442  0.0261 0.9990  812 -3.4129 -0.1877
## 1119 Detection           Red-shouldered Hawk  Intercept -2.6709 0.5866 -3.6697 -2.7314 -1.4228 1.0163  420 -3.5466 -1.6617
## 1120 Detection               Red-tailed Hawk  Intercept -2.3845 0.6453 -3.6028 -2.3783 -1.1120 1.0280  402 -3.4122 -1.3376
## 1121 Detection     Ruby-throated Hummingbird  Intercept -2.4496 0.2736 -2.9486 -2.4767 -1.8809 1.0004  820 -2.8826 -1.9897
## 1122 Detection          Red-winged Blackbird  Intercept  0.5980 0.2025  0.2198  0.5905  0.9998 1.0003 1462  0.2770  0.9475
## 1123 Detection              Savannah Sparrow  Intercept -0.5520 1.0493 -2.7143 -0.5236  1.3909 0.9996 1200 -2.3353  1.1310
## 1124 Detection               Scarlet Tanager  Intercept -0.5934 0.1628 -0.9025 -0.6039 -0.2612 1.0033 1200 -0.8566 -0.3162
## 1125 Detection                  Song Sparrow  Intercept  0.8645 0.1554  0.5658  0.8678  1.1596 1.0001 1200  0.6153  1.1076
## 1126 Detection                 Swamp Sparrow  Intercept  0.3635 0.5625 -0.7266  0.3428  1.4658 1.0023 1351 -0.5748  1.2995
## 1127 Detection             Tennessee Warbler  Intercept -1.4303 1.3505 -4.0629 -1.4535  1.2601 1.0007  832 -3.6931  0.7485
## 1128 Detection                  Tree Swallow  Intercept -0.8026 0.5309 -1.8999 -0.7871  0.2283 0.9998 1200 -1.7292  0.0371
## 1129 Detection               Tufted Titmouse  Intercept  0.6576 0.1113  0.4539  0.6615  0.8861 1.0028 1368  0.4778  0.8455
## 1130 Detection                Turkey Vulture  Intercept -2.4491 0.6222 -3.6384 -2.4809 -1.1709 1.0005  681 -3.4272 -1.3834
## 1131 Detection                         Veery  Intercept -1.2947 0.5228 -2.3640 -1.2833 -0.3025 1.0060  994 -2.1902 -0.4173
## 1132 Detection                 Virginia Rail  Intercept -1.4806 1.3193 -4.0210 -1.5112  1.1589 1.0070  881 -3.6123  0.7821
## 1133 Detection                Warbling Vireo  Intercept -0.0244 0.2801 -0.5786 -0.0177  0.4980 1.0198 1200 -0.4968  0.4227
## 1134 Detection       White-breasted Nuthatch  Intercept -0.2800 0.1261 -0.5327 -0.2818 -0.0251 1.0007 1200 -0.4849 -0.0705
## 1135 Detection              White-eyed Vireo  Intercept  0.1657 0.9943 -1.8028  0.1673  2.1732 1.0055 1096 -1.4582  1.8157
## 1136 Detection             Willow Flycatcher  Intercept -0.2385 0.4419 -1.1316 -0.2300  0.5933 1.0092 1200 -1.0006  0.4597
## 1137 Detection                   Wild Turkey  Intercept -2.3893 0.9984 -4.4171 -2.3021 -0.6552 1.0080  311 -4.1397 -0.8417
## 1138 Detection                   Winter Wren  Intercept -0.9300 0.9364 -2.8922 -0.9029  0.7728 1.0092  984 -2.5027  0.5341
## 1139 Detection                     Wood Duck  Intercept -1.9061 0.9914 -3.8993 -1.8636 -0.0854 1.0003  791 -3.6356 -0.3322
## 1140 Detection                   Wood Thrush  Intercept -0.2613 0.1573 -0.5751 -0.2575  0.0385 1.0015 1200 -0.5351 -0.0080
## 1141 Detection          Yellow-billed Cuckoo  Intercept -2.4364 0.8146 -4.0035 -2.4027 -0.8602 1.0191  496 -3.8012 -1.1591
## 1142 Detection                Yellow Warbler  Intercept -0.0640 0.2214 -0.4793 -0.0699  0.3739 1.0190 1200 -0.4373  0.3085
## 1143 Detection         Yellow-throated Vireo  Intercept -1.6012 0.5299 -2.7454 -1.5778 -0.6005 1.0231  732 -2.5139 -0.7716
## 1144 Detection       Yellow-throated Warbler  Intercept -1.4045 0.7624 -3.1879 -1.3652 -0.0613 1.0388  659 -2.7397 -0.2909
## 1145 Detection            Acadian Flycatcher        day  0.0986 0.1299 -0.1620  0.0974  0.3501 1.0097 1200 -0.1108  0.3090
## 1146 Detection              Alder Flycatcher        day  0.1548 0.1907 -0.2162  0.1515  0.5384 1.0110 1200 -0.1460  0.4681
## 1147 Detection                 American Crow        day  0.2758 0.1274  0.0261  0.2783  0.5125 1.0226 1200  0.0683  0.4826
## 1148 Detection            American Goldfinch        day  0.1236 0.0948 -0.0643  0.1209  0.3082 1.0025 1200 -0.0330  0.2791
## 1149 Detection              American Kestrel        day  0.1259 0.1885 -0.2469  0.1250  0.4948 0.9995 1672 -0.1835  0.4366
## 1150 Detection             American Redstart        day  0.2591 0.1801 -0.0751  0.2534  0.6358 1.0061 1200 -0.0274  0.5698
## 1151 Detection                American Robin        day  0.1985 0.1031 -0.0106  0.1987  0.4087 1.0084 1200  0.0309  0.3653
## 1152 Detection             American Woodcock        day  0.1477 0.1943 -0.2175  0.1477  0.5366 1.0007 1200 -0.1613  0.4713
## 1153 Detection                    Barred Owl        day  0.1989 0.1841 -0.1593  0.1993  0.5642 1.0188 1302 -0.0924  0.5102
## 1154 Detection                    Bald Eagle        day  0.1948 0.1886 -0.1723  0.1922  0.5686 1.0088 1200 -0.1007  0.5019
## 1155 Detection                  Bank Swallow        day  0.1410 0.1906 -0.2373  0.1405  0.5087 1.0075 1200 -0.1695  0.4358
## 1156 Detection              Baltimore Oriole        day  0.0835 0.1209 -0.1618  0.0795  0.3294 1.0020 1200 -0.1202  0.2819
## 1157 Detection                  Barn Swallow        day  0.0631 0.1707 -0.2740  0.0610  0.3950 1.0233 1200 -0.2264  0.3399
## 1158 Detection        Black-capped Chickadee        day  0.0724 0.0915 -0.1093  0.0735  0.2450 1.0096 1200 -0.0766  0.2151
## 1159 Detection             Belted Kingfisher        day  0.1565 0.1543 -0.1588  0.1595  0.4464 1.0025 1200 -0.1037  0.4088
## 1160 Detection         Blue-gray Gnatcatcher        day -0.0466 0.1115 -0.2621 -0.0479  0.1718 1.0093 1200 -0.2290  0.1348
## 1161 Detection          Brown-headed Cowbird        day  0.3673 0.0988  0.1788  0.3687  0.5529 1.0020 1200  0.2049  0.5261
## 1162 Detection             Blue-headed Vireo        day  0.1432 0.1911 -0.2252  0.1477  0.5038 1.0073 1200 -0.1828  0.4529
## 1163 Detection                      Blue Jay        day  0.0628 0.0956 -0.1202  0.0610  0.2445 1.0074 1200 -0.0973  0.2169
## 1164 Detection                      Bobolink        day  0.1557 0.2006 -0.2438  0.1543  0.5544 1.0007 1200 -0.1857  0.4810
## 1165 Detection                 Brown Creeper        day  0.1780 0.1771 -0.1775  0.1811  0.5287 1.0122 1200 -0.1129  0.4592
## 1166 Detection                Brown Thrasher        day  0.1293 0.1908 -0.2394  0.1331  0.5144 1.0037 1092 -0.1882  0.4368
## 1167 Detection  Black-throated Green Warbler        day  0.1595 0.1965 -0.2156  0.1617  0.5583 1.0111 1200 -0.1636  0.4785
## 1168 Detection             Broad-winged Hawk        day  0.1484 0.1904 -0.2413  0.1524  0.5318 0.9993 1116 -0.1660  0.4685
## 1169 Detection           Blue-winged Warbler        day  0.1561 0.1892 -0.2066  0.1578  0.5257 1.0033 1200 -0.1517  0.4649
## 1170 Detection                  Canada Goose        day  0.0339 0.1743 -0.2971  0.0407  0.3792 1.0063  943 -0.2509  0.3244
## 1171 Detection                 Carolina Wren        day  0.4324 0.1389  0.1634  0.4303  0.7192 1.0065 1069  0.2114  0.6742
## 1172 Detection                 Cedar Waxwing        day  0.2097 0.1273 -0.0452  0.2059  0.4551 0.9999 1188 -0.0052  0.4169
## 1173 Detection              Cerulean Warbler        day  0.1511 0.1947 -0.2362  0.1520  0.5287 1.0025 1200 -0.1582  0.4796
## 1174 Detection              Chipping Sparrow        day  0.2403 0.1375 -0.0231  0.2423  0.5171 1.0259 1200  0.0169  0.4611
## 1175 Detection                 Chimney Swift        day  0.0787 0.1125 -0.1357  0.0780  0.3080 1.0017 1485 -0.1078  0.2574
## 1176 Detection                 Cliff Swallow        day  0.1697 0.1842 -0.1976  0.1720  0.5239 1.0043 1200 -0.1416  0.4830
## 1177 Detection                Common Grackle        day  0.3979 0.1222  0.1662  0.3953  0.6522 1.0132 1200  0.1997  0.6016
## 1178 Detection                 Cooper's Hawk        day  0.2095 0.1771 -0.1385  0.2106  0.5531 1.0231 1200 -0.0852  0.5025
## 1179 Detection           Common Yellowthroat        day  0.1218 0.1462 -0.1653  0.1223  0.4243 1.0059 1200 -0.1246  0.3708
## 1180 Detection               Dark-eyed Junco        day  0.0171 0.1786 -0.3546  0.0249  0.3473 1.0008 1200 -0.2964  0.3007
## 1181 Detection              Downy Woodpecker        day  0.3473 0.0991  0.1543  0.3478  0.5370 0.9994 1200  0.1850  0.5131
## 1182 Detection              Eastern Bluebird        day  0.1384 0.1414 -0.1378  0.1362  0.4105 1.0004 1200 -0.1013  0.3627
## 1183 Detection              Eastern Kingbird        day  0.0506 0.1784 -0.2953  0.0543  0.3817 1.0003 1200 -0.2354  0.3519
## 1184 Detection            Eastern Meadowlark        day  0.1104 0.2013 -0.3062  0.1139  0.5019 1.0047 1103 -0.2216  0.4254
## 1185 Detection                Eastern Phoebe        day -0.0853 0.1945 -0.4505 -0.0828  0.2973 1.0038 1200 -0.3877  0.2299
## 1186 Detection                Eastern Towhee        day  0.1447 0.1517 -0.1573  0.1454  0.4420 1.0037 1200 -0.0981  0.3883
## 1187 Detection            Eastern Wood-Pewee        day  0.3671 0.1041  0.1791  0.3655  0.5767 1.0016 1200  0.2075  0.5415
## 1188 Detection             European Starling        day  0.0247 0.1577 -0.2911  0.0320  0.3039 1.0016 1200 -0.2459  0.2757
## 1189 Detection                 Field Sparrow        day  0.1501 0.1917 -0.2314  0.1531  0.5257 1.0006 1180 -0.1756  0.4541
## 1190 Detection              Great Blue Heron        day  0.0814 0.1784 -0.2621  0.0862  0.4252 1.0012 1504 -0.2257  0.3828
## 1191 Detection      Great Crested Flycatcher        day  0.0853 0.1048 -0.1257  0.0864  0.2819 0.9994 1200 -0.0881  0.2496
## 1192 Detection              Great Horned Owl        day  0.1706 0.1915 -0.2270  0.1683  0.5468 1.0055 1200 -0.1407  0.4864
## 1193 Detection                  Gray Catbird        day  0.1427 0.1172 -0.0908  0.1463  0.3660 1.0056 1582 -0.0554  0.3302
## 1194 Detection                   Green Heron        day  0.1389 0.1983 -0.2827  0.1426  0.5210 1.0041 1200 -0.2018  0.4517
## 1195 Detection              Hairy Woodpecker        day  0.0755 0.1260 -0.1757  0.0741  0.3162 1.0025 1200 -0.1286  0.2835
## 1196 Detection                  Herring Gull        day  0.1133 0.1971 -0.2865  0.1225  0.4912 1.0067 1200 -0.2042  0.4216
## 1197 Detection                 Hermit Thrush        day  0.1010 0.1953 -0.2825  0.1023  0.4777 1.0053 1200 -0.2255  0.4120
## 1198 Detection                   House Finch        day  0.1856 0.1424 -0.0998  0.1853  0.4573 1.0038 1200 -0.0589  0.4133
## 1199 Detection                 House Sparrow        day  0.0428 0.1519 -0.2631  0.0467  0.3435 1.0057 1200 -0.2100  0.2898
## 1200 Detection                Hooded Warbler        day  0.0571 0.1460 -0.2221  0.0572  0.3382 1.0051 1200 -0.1793  0.2920
## 1201 Detection                    House Wren        day -0.0729 0.1284 -0.3267 -0.0702  0.1752 1.0012 1200 -0.2888  0.1382
## 1202 Detection                Indigo Bunting        day  0.1900 0.1280 -0.0554  0.1899  0.4470 1.0026 1200 -0.0222  0.4105
## 1203 Detection                      Killdeer        day  0.0560 0.1881 -0.3172  0.0576  0.3994 1.0043 1200 -0.2546  0.3550
## 1204 Detection         Louisiana Waterthrush        day  0.1160 0.1744 -0.2203  0.1084  0.4660 0.9992 1200 -0.1658  0.4054
## 1205 Detection                       Mallard        day  0.1845 0.1802 -0.1570  0.1846  0.5571 1.0014 1200 -0.1079  0.4796
## 1206 Detection                 Mourning Dove        day  0.1588 0.1550 -0.1401  0.1529  0.4773 1.0001 1200 -0.0912  0.4193
## 1207 Detection             Northern Cardinal        day  0.2735 0.0982  0.0827  0.2746  0.4557 1.0025 1105  0.1070  0.4319
## 1208 Detection              Northern Flicker        day  0.2229 0.1235 -0.0176  0.2252  0.4677 1.0049 1270  0.0259  0.4268
## 1209 Detection               Northern Parula        day  0.1401 0.1913 -0.2682  0.1474  0.4926 1.0044 1302 -0.1947  0.4449
## 1210 Detection Northern Rough-winged Swallow        day  0.0534 0.1752 -0.3095  0.0581  0.3880 0.9996 1200 -0.2405  0.3437
## 1211 Detection                Orchard Oriole        day  0.2420 0.1737 -0.1047  0.2450  0.5967 1.0038 1200 -0.0377  0.5371
## 1212 Detection                      Ovenbird        day  0.1345 0.1834 -0.2181  0.1314  0.4997 0.9997 1667 -0.1569  0.4412
## 1213 Detection           Pileated Woodpecker        day  0.1726 0.1249 -0.0609  0.1726  0.4227 1.0012 1157 -0.0322  0.3837
## 1214 Detection                  Purple Finch        day  0.1579 0.1877 -0.2041  0.1617  0.5314 1.0000 1200 -0.1515  0.4636
## 1215 Detection                 Purple Martin        day  0.1504 0.1926 -0.2434  0.1569  0.5312 1.0023 1200 -0.1650  0.4727
## 1216 Detection        Rose-breasted Grosbeak        day  0.1900 0.1351 -0.0729  0.1884  0.4645 1.0036 1200 -0.0237  0.4086
## 1217 Detection              Ring-billed Gull        day  0.0756 0.1694 -0.2487  0.0833  0.4050 1.0067 1200 -0.2062  0.3400
## 1218 Detection         Red-breasted Nuthatch        day  0.1516 0.2019 -0.2571  0.1478  0.5503 1.0126 1200 -0.1880  0.4774
## 1219 Detection        Red-bellied Woodpecker        day  0.3040 0.0928  0.1197  0.3019  0.4813 1.0016 1193  0.1455  0.4586
## 1220 Detection                Red-eyed Vireo        day  0.0933 0.1003 -0.0941  0.0907  0.2963 1.0053 1200 -0.0651  0.2646
## 1221 Detection         Red-headed Woodpecker        day  0.2552 0.1811 -0.0847  0.2500  0.6102 1.0004 1200 -0.0330  0.5680
## 1222 Detection                   Rock Pigeon        day  0.1358 0.1957 -0.2678  0.1370  0.5400 1.0005 1200 -0.1855  0.4507
## 1223 Detection           Red-shouldered Hawk        day  0.0209 0.1654 -0.3230  0.0300  0.3223 1.0162 1200 -0.2537  0.2730
## 1224 Detection               Red-tailed Hawk        day  0.2736 0.1655 -0.0570  0.2773  0.6062 1.0009 1200  0.0019  0.5463
## 1225 Detection     Ruby-throated Hummingbird        day  0.3801 0.1410  0.1119  0.3788  0.6603 1.0187 1200  0.1629  0.6246
## 1226 Detection          Red-winged Blackbird        day  0.2444 0.1374 -0.0399  0.2454  0.4948 1.0015 1475  0.0194  0.4566
## 1227 Detection              Savannah Sparrow        day  0.1181 0.1954 -0.2763  0.1216  0.5060 1.0001 1200 -0.2083  0.4512
## 1228 Detection               Scarlet Tanager        day  0.0283 0.1184 -0.1939  0.0304  0.2624 1.0016 1200 -0.1588  0.2176
## 1229 Detection                  Song Sparrow        day  0.1966 0.1187 -0.0316  0.1915  0.4472 1.0005 1200  0.0096  0.3906
## 1230 Detection                 Swamp Sparrow        day  0.1754 0.1891 -0.1932  0.1689  0.5411 1.0065 1200 -0.1327  0.4755
## 1231 Detection             Tennessee Warbler        day  0.1543 0.1983 -0.2366  0.1573  0.5376 1.0063 1332 -0.1849  0.4678
## 1232 Detection                  Tree Swallow        day  0.1621 0.1910 -0.2358  0.1578  0.5437 1.0017 1281 -0.1592  0.4862
## 1233 Detection               Tufted Titmouse        day  0.3810 0.0953  0.1928  0.3797  0.5694 1.0029 1311  0.2217  0.5420
## 1234 Detection                Turkey Vulture        day  0.0614 0.1675 -0.2675  0.0646  0.3712 1.0039 1200 -0.2295  0.3342
## 1235 Detection                         Veery        day  0.2025 0.1713 -0.1325  0.1966  0.5545 1.0064 1200 -0.0712  0.4931
## 1236 Detection                 Virginia Rail        day  0.1511 0.1936 -0.2239  0.1488  0.5321 1.0030 1200 -0.1634  0.4742
## 1237 Detection                Warbling Vireo        day  0.2303 0.1550 -0.0716  0.2332  0.5427 1.0013 1200 -0.0273  0.4853
## 1238 Detection       White-breasted Nuthatch        day  0.1409 0.0956 -0.0542  0.1409  0.3141 1.0052 1200 -0.0248  0.2914
## 1239 Detection              White-eyed Vireo        day  0.2214 0.1905 -0.1614  0.2197  0.5878 1.0018 1200 -0.0934  0.5350
## 1240 Detection             Willow Flycatcher        day  0.0734 0.1963 -0.3209  0.0721  0.4324 1.0048 1200 -0.2409  0.3857
## 1241 Detection                   Wild Turkey        day  0.1162 0.1834 -0.2628  0.1182  0.4775 1.0142 1200 -0.1851  0.4096
## 1242 Detection                   Winter Wren        day  0.1040 0.2001 -0.3012  0.1110  0.4837 0.9995 1323 -0.2410  0.4273
## 1243 Detection                     Wood Duck        day  0.1731 0.1901 -0.2018  0.1685  0.5375 1.0038 1200 -0.1379  0.4693
## 1244 Detection                   Wood Thrush        day  0.1821 0.1110 -0.0391  0.1823  0.3931 1.0076 1200  0.0048  0.3656
## 1245 Detection          Yellow-billed Cuckoo        day  0.1904 0.1809 -0.1687  0.1925  0.5317 1.0014 1200 -0.1030  0.4812
## 1246 Detection                Yellow Warbler        day  0.1565 0.1385 -0.1216  0.1544  0.4208 1.0016 1099 -0.0736  0.3866
## 1247 Detection         Yellow-throated Vireo        day  0.2005 0.1719 -0.1458  0.1972  0.5379 1.0007 1100 -0.0861  0.4785
## 1248 Detection       Yellow-throated Warbler        day  0.1073 0.1801 -0.2720  0.1117  0.4474 1.0124 1200 -0.1984  0.4009

covariates by migratory status